Sequence Distance

I am sort of confused on how matlab gets its answers for various distance methods. My boss wants to know how matlab arrives at various answers.

I set up matlab to give me answers in fractions, so when I analyze two sequences of the same length, it gives me the denominator of the fraction to be length of the sequences (for example, if both amino acid sequences have a length of 327 then the answer has a denominator of 327). I understood this until when I analyzed two amino acid sequences with each having a different length, one being 369 amino acids long, and another being 379 amino acids long. It gave me the answer: 209/398. I don't understand how it got to having a denominator of 398 (I specifically asked it to use p-distance). When I type in "help seqpdist", it does not give me very clear explanation on how the p-distance works.

So can some one please help me out? I would greatly appreciate it!

Answer 1

[Lucio Cetto]

When you are comparing sequences it is common to first align them using a dynamic programing algorithm. SEQPDIST uses NWALIGN to pair-wise align all possible pairs of sequences and then takes the measure from the alignment.

Consider:

seqpdist({'AACGT','AAGT','AAT'},'alpha','nt','square',1,'method','p-dist')

The alignment between 1 and 2 is 'AACGT' and 'AA-GT' =>1/5

The alignment between 1 and 3 is 'AACGT' and 'AA--T' =>2/5

The alignment between 1 and 3 is 'AAGT' and 'AA-T' =>1/4

HTH