{"group":{"id":1,"name":"Community","lockable":false,"created_at":"2012-01-18T18:02:15.000Z","updated_at":"2025-12-14T01:33:56.000Z","description":"Problems submitted by members of the MATLAB Central community.","is_default":true,"created_by":161519,"badge_id":null,"featured":false,"trending":false,"solution_count_in_trending_period":0,"trending_last_calculated":"2025-12-14T00:00:00.000Z","image_id":null,"published":true,"community_created":false,"status_id":2,"is_default_group_for_player":false,"deleted_by":null,"deleted_at":null,"restored_by":null,"restored_at":null,"description_opc":null,"description_html":null,"published_at":null},"problems":[{"id":912,"title":"Genome Sequence 002: Introductory DNA Sequencing (Flipped Segments)","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssTACAGGTACCGGssss Middle\r\nsssssGGCCATGGACATssss Middle Reversed\r\nssssssssssssGACATTACG\r\nGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\r\nSegments may be flipped (Genome_002 change)\r\nLength of each segment - 48\r\nSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\nAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order will be scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\r\nExample: [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\r\nFuture: Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 727.2px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.6px; transform-origin: 407px 363.6px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 367px 8px; transform-origin: 367px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssTACAGGTACCGGssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 148px 8.5px; transform-origin: 148px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssGGCCATGGACATssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 60px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 60px 8.5px; \"\u003eMiddle Reversed\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 384px 8px; transform-origin: 384px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 155px 8px; transform-origin: 155px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be flipped (Genome_002 change)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 241px 8px; transform-origin: 241px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 324px 8px; transform-origin: 324px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order will be scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 184px 8px; transform-origin: 184px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 317px 8px; transform-origin: 317px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n  G=[];\r\nend","test_suite":"%%\r\ntic\r\nL=4176; % 1040  Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1  % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n% Flip random segments\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1  % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":5,"test_suite_updated_at":"2021-07-16T14:47:06.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-08-15T19:14:39.000Z","updated_at":"2021-07-16T14:47:06.000Z","published_at":"2012-10-01T03:42:15.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssTACAGGTACCGGssss Middle\\nsssssGGCCATGGACATssss Middle Reversed\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be flipped (Genome_002 change)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":863,"title":"Genome Sequence 001: Introductory DNA Sequencing","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. \u003chttp://en.wikipedia.org/wiki/Genome DNA Sequencing\u003e and the \u003chttp://en.wikipedia.org/wiki/Shotgun_sequencing Shot Gun Method\u003e will be naively simplified into Cody Challenges. \u003chttp://en.wikipedia.org/wiki/Genome_sequence Genome sizes\u003e is another interesting wiki page.\r\n\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123.  The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.  \r\n\r\n*Example:* G = ACGTCGGCCATGGACATTACG\r\n\r\nGiven three overlapping pieces,  ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\r\n\r\n  ACGTCGGCCATGGACATTACG\r\n  ACGTCGGCCAsssssssssss\r\n  sssssGGCCATGGACATssss\r\n  ssssssssssssGACATTACG\r\n\r\n\r\n\r\nGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\r\n\r\n# Length of each segment - 48\r\n# Segments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\n# All segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\n# Segments read left to right (no flips)\r\n# No errors in the segments\r\n# Genome is random (No duplicate starts or ends for 16 symbols of segments)\r\n# Segments will be scrambled\r\n\r\n*Input:* segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\n\r\n*Output:* Gout, Genome vector of values [0,1,2,3]\r\n\r\n*Example:* [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\r\n\r\n*Future:* Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)","description_html":"\u003cp\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing. \u003ca href=\"http://en.wikipedia.org/wiki/Genome\"\u003eDNA Sequencing\u003c/a\u003e and the \u003ca href=\"http://en.wikipedia.org/wiki/Shotgun_sequencing\"\u003eShot Gun Method\u003c/a\u003e will be naively simplified into Cody Challenges. \u003ca href=\"http://en.wikipedia.org/wiki/Genome_sequence\"\u003eGenome sizes\u003c/a\u003e is another interesting wiki page.\u003c/p\u003e\u003cp\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123.  The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e G = ACGTCGGCCATGGACATTACG\u003c/p\u003e\u003cp\u003eGiven three overlapping pieces,  ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003eACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssGGCCATGGACATssss\r\nssssssssssssGACATTACG\r\n\u003c/pre\u003e\u003cp\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/p\u003e\u003col\u003e\u003cli\u003eLength of each segment - 48\u003c/li\u003e\u003cli\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/li\u003e\u003cli\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/li\u003e\u003cli\u003eSegments read left to right (no flips)\u003c/li\u003e\u003cli\u003eNo errors in the segments\u003c/li\u003e\u003cli\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/li\u003e\u003cli\u003eSegments will be scrambled\u003c/li\u003e\u003c/ol\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Gout, Genome vector of values [0,1,2,3]\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/p\u003e\u003cp\u003e\u003cb\u003eFuture:\u003c/b\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/p\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n  G=[];\r\nend","test_suite":"tic\r\nL=4176; % 1040  Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1  % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1  % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":6,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":7,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-24T19:18:06.000Z","updated_at":"2012-10-01T00:04:58.000Z","published_at":"2012-10-01T00:04:58.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Shotgun_sequencing\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome_sequence\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e G = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssGGCCATGGACATssss\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments read left to right (no flips)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"}],"problem_search":{"errors":[],"problems":[{"id":912,"title":"Genome Sequence 002: Introductory DNA Sequencing (Flipped Segments)","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssTACAGGTACCGGssss Middle\r\nsssssGGCCATGGACATssss Middle Reversed\r\nssssssssssssGACATTACG\r\nGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\r\nSegments may be flipped (Genome_002 change)\r\nLength of each segment - 48\r\nSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\nAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order will be scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\r\nExample: [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\r\nFuture: Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 727.2px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.6px; transform-origin: 407px 363.6px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 367px 8px; transform-origin: 367px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssTACAGGTACCGGssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 148px 8.5px; transform-origin: 148px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssGGCCATGGACATssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 60px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 60px 8.5px; \"\u003eMiddle Reversed\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 384px 8px; transform-origin: 384px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 155px 8px; transform-origin: 155px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be flipped (Genome_002 change)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 241px 8px; transform-origin: 241px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 324px 8px; transform-origin: 324px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order will be scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 184px 8px; transform-origin: 184px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 317px 8px; transform-origin: 317px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n  G=[];\r\nend","test_suite":"%%\r\ntic\r\nL=4176; % 1040  Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1  % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n% Flip random segments\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1  % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":5,"test_suite_updated_at":"2021-07-16T14:47:06.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-08-15T19:14:39.000Z","updated_at":"2021-07-16T14:47:06.000Z","published_at":"2012-10-01T03:42:15.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssTACAGGTACCGGssss Middle\\nsssssGGCCATGGACATssss Middle Reversed\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be flipped (Genome_002 change)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":863,"title":"Genome Sequence 001: Introductory DNA Sequencing","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. \u003chttp://en.wikipedia.org/wiki/Genome DNA Sequencing\u003e and the \u003chttp://en.wikipedia.org/wiki/Shotgun_sequencing Shot Gun Method\u003e will be naively simplified into Cody Challenges. \u003chttp://en.wikipedia.org/wiki/Genome_sequence Genome sizes\u003e is another interesting wiki page.\r\n\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123.  The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.  \r\n\r\n*Example:* G = ACGTCGGCCATGGACATTACG\r\n\r\nGiven three overlapping pieces,  ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\r\n\r\n  ACGTCGGCCATGGACATTACG\r\n  ACGTCGGCCAsssssssssss\r\n  sssssGGCCATGGACATssss\r\n  ssssssssssssGACATTACG\r\n\r\n\r\n\r\nGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\r\n\r\n# Length of each segment - 48\r\n# Segments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\n# All segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\n# Segments read left to right (no flips)\r\n# No errors in the segments\r\n# Genome is random (No duplicate starts or ends for 16 symbols of segments)\r\n# Segments will be scrambled\r\n\r\n*Input:* segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\n\r\n*Output:* Gout, Genome vector of values [0,1,2,3]\r\n\r\n*Example:* [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\r\n\r\n*Future:* Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)","description_html":"\u003cp\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing. \u003ca href=\"http://en.wikipedia.org/wiki/Genome\"\u003eDNA Sequencing\u003c/a\u003e and the \u003ca href=\"http://en.wikipedia.org/wiki/Shotgun_sequencing\"\u003eShot Gun Method\u003c/a\u003e will be naively simplified into Cody Challenges. \u003ca href=\"http://en.wikipedia.org/wiki/Genome_sequence\"\u003eGenome sizes\u003c/a\u003e is another interesting wiki page.\u003c/p\u003e\u003cp\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123.  The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e G = ACGTCGGCCATGGACATTACG\u003c/p\u003e\u003cp\u003eGiven three overlapping pieces,  ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003eACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssGGCCATGGACATssss\r\nssssssssssssGACATTACG\r\n\u003c/pre\u003e\u003cp\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/p\u003e\u003col\u003e\u003cli\u003eLength of each segment - 48\u003c/li\u003e\u003cli\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/li\u003e\u003cli\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/li\u003e\u003cli\u003eSegments read left to right (no flips)\u003c/li\u003e\u003cli\u003eNo errors in the segments\u003c/li\u003e\u003cli\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/li\u003e\u003cli\u003eSegments will be scrambled\u003c/li\u003e\u003c/ol\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Gout, Genome vector of values [0,1,2,3]\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/p\u003e\u003cp\u003e\u003cb\u003eFuture:\u003c/b\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/p\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n  G=[];\r\nend","test_suite":"tic\r\nL=4176; % 1040  Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1  % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1  % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":6,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":7,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-24T19:18:06.000Z","updated_at":"2012-10-01T00:04:58.000Z","published_at":"2012-10-01T00:04:58.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Shotgun_sequencing\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome_sequence\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e G = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssGGCCATGGACATssss\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments read left to right (no flips)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"}],"term":"tag:\"link list\"","current_player_id":null,"fields":[{"name":"page","type":"integer","callback":null,"default":1,"directive":null,"facet":null,"facet_method":"and","operator":null,"param":null,"static":null,"prepend":true},{"name":"per_page","type":"integer","callback":null,"default":50,"directive":null,"facet":null,"facet_method":"and","operator":null,"param":null,"static":null,"prepend":true},{"name":"sort","type":"string","callback":null,"default":null,"directive":null,"facet":null,"facet_method":"and","operator":null,"param":null,"static":null,"prepend":true},{"name":"body","type":"text","callback":null,"default":"*:*","directive":null,"facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":false},{"name":"group","type":"string","callback":null,"default":null,"directive":"group","facet":true,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"difficulty_rating_bin","type":"string","callback":null,"default":null,"directive":"difficulty_rating_bin","facet":true,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"id","type":"integer","callback":null,"default":null,"directive":"id","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"tag","type":"string","callback":null,"default":null,"directive":"tag","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"product","type":"string","callback":null,"default":null,"directive":"product","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"created_at","type":"timeframe","callback":{},"default":null,"directive":"created_at","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"profile_id","type":"integer","callback":null,"default":null,"directive":"author_id","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"created_by","type":"string","callback":null,"default":null,"directive":"author","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"player_id","type":"integer","callback":null,"default":null,"directive":"solver_id","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"player","type":"string","callback":null,"default":null,"directive":"solver","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"solvers_count","type":"integer","callback":null,"default":null,"directive":"solvers_count","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"comments_count","type":"integer","callback":null,"default":null,"directive":"comments_count","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"likes_count","type":"integer","callback":null,"default":null,"directive":"likes_count","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"leader_id","type":"integer","callback":null,"default":null,"directive":"leader_id","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true},{"name":"leading_solution","type":"integer","callback":null,"default":null,"directive":"leading_solution","facet":null,"facet_method":"and","operator":null,"param":"term","static":null,"prepend":true}],"filters":[{"name":"asset_type","type":"string","callback":null,"default":null,"directive":null,"facet":null,"facet_method":"and","operator":null,"param":null,"static":"\"cody:problem\"","prepend":true},{"name":"profile_id","type":"integer","callback":{},"default":null,"directive":null,"facet":null,"facet_method":"and","operator":null,"param":"author_id","static":null,"prepend":true}],"query":{"params":{"per_page":50,"term":"tag:\"link list\"","current_player":null,"sort":"map(difficulty_value,0,0,999) asc"},"parser":"MathWorks::Search::Solr::QueryParser","directives":{"term":{"directives":{"tag":[["tag:\"link list\"","","\"","link list","\""]]}}},"facets":{"#\u003cMathWorks::Search::Field:0x00007f1968977308\u003e":null,"#\u003cMathWorks::Search::Field:0x00007f1968977268\u003e":null},"filters":{"#\u003cMathWorks::Search::Field:0x00007f1968974ec8\u003e":"\"cody:problem\""},"fields":{"#\u003cMathWorks::Search::Field:0x00007f1968977768\u003e":1,"#\u003cMathWorks::Search::Field:0x00007f1968977588\u003e":50,"#\u003cMathWorks::Search::Field:0x00007f19689774e8\u003e":"map(difficulty_value,0,0,999) asc","#\u003cMathWorks::Search::Field:0x00007f19689773a8\u003e":"tag:\"link list\""},"user_query":{"#\u003cMathWorks::Search::Field:0x00007f19689773a8\u003e":"tag:\"link list\""},"queried_facets":{}},"query_backend":{"connection":{"configuration":{"index_url":"http://index-op-v2/solr/","query_url":"http://search-op-v2/solr/","direct_access_index_urls":["http://index-op-v2/solr/"],"direct_access_query_urls":["http://search-op-v2/solr/"],"timeout":10,"vhost":"search","exchange":"search.topic","heartbeat":30,"pre_index_mode":false,"host":"rabbitmq-eks","port":5672,"username":"search","password":"J3bGPZzQ7asjJcCk","virtual_host":"search","indexer":"amqp","http_logging":"true","core":"cody"},"query_connection":{"uri":"http://search-op-v2/solr/cody/","proxy":null,"connection":{"parallel_manager":null,"headers":{"User-Agent":"Faraday v1.0.1"},"params":{},"options":{"params_encoder":"Faraday::FlatParamsEncoder","proxy":null,"bind":null,"timeout":null,"open_timeout":null,"read_timeout":null,"write_timeout":null,"boundary":null,"oauth":null,"context":null,"on_data":null},"ssl":{"verify":true,"ca_file":null,"ca_path":null,"verify_mode":null,"cert_store":null,"client_cert":null,"client_key":null,"certificate":null,"private_key":null,"verify_depth":null,"version":null,"min_version":null,"max_version":null},"default_parallel_manager":null,"builder":{"adapter":{"name":"Faraday::Adapter::NetHttp","args":[],"block":null},"handlers":[{"name":"Faraday::Response::RaiseError","args":[],"block":null}],"app":{"app":{"ssl_cert_store":{"verify_callback":null,"error":null,"error_string":null,"chain":null,"time":null},"app":{},"connection_options":{},"config_block":null}}},"url_prefix":"http://search-op-v2/solr/cody/","manual_proxy":false,"proxy":null},"update_format":"RSolr::JSON::Generator","update_path":"update","options":{"url":"http://search-op-v2/solr/cody"}}},"query":{"params":{"per_page":50,"term":"tag:\"link list\"","current_player":null,"sort":"map(difficulty_value,0,0,999) asc"},"parser":"MathWorks::Search::Solr::QueryParser","directives":{"term":{"directives":{"tag":[["tag:\"link list\"","","\"","link list","\""]]}}},"facets":{"#\u003cMathWorks::Search::Field:0x00007f1968977308\u003e":null,"#\u003cMathWorks::Search::Field:0x00007f1968977268\u003e":null},"filters":{"#\u003cMathWorks::Search::Field:0x00007f1968974ec8\u003e":"\"cody:problem\""},"fields":{"#\u003cMathWorks::Search::Field:0x00007f1968977768\u003e":1,"#\u003cMathWorks::Search::Field:0x00007f1968977588\u003e":50,"#\u003cMathWorks::Search::Field:0x00007f19689774e8\u003e":"map(difficulty_value,0,0,999) asc","#\u003cMathWorks::Search::Field:0x00007f19689773a8\u003e":"tag:\"link list\""},"user_query":{"#\u003cMathWorks::Search::Field:0x00007f19689773a8\u003e":"tag:\"link list\""},"queried_facets":{}},"options":{"fields":["id","difficulty_rating"]},"join":" "},"results":[{"id":912,"difficulty_rating":"medium"},{"id":863,"difficulty_rating":"medium"}]}}