blosum

Return BLOSUM scoring matrix

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Syntax

Matrix = blosum(Identity)
[Matrix,MatrixInfo] = blosum(Identity)
___ = blosum(Identity,Name=Value)

Description

Matrix = blosum(Identity) returns a BLOSUM (Blocks Substitution Matrix) scoring matrix with a specified percent identity. The default ordering of the output includes the extended characters B, Z, X, and *. The order is: A R N D C Q E G H I L K M F P S T W Y V B Z X *

example

[Matrix,MatrixInfo] = blosum(Identity) returns MatrixInfo, a structure of information about Matrix, a BLOSUM matrix.

___ = blosum(Identity,Name=Value) uses additional options specified by one or more name-value arguments.

Examples

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Open Live Script

Return a BLOSUM matrix with a percent identity level of 50.

B50 = blosum(50)
B50 = 24×24

     5    -2    -1    -2    -1    -1    -1     0    -2    -1    -2    -1    -1    -3    -1     1     0    -3    -2     0    -2    -1    -1    -5
    -2     7    -1    -2    -4     1     0    -3     0    -4    -3     3    -2    -3    -3    -1    -1    -3    -1    -3    -1     0    -1    -5
    -1    -1     7     2    -2     0     0     0     1    -3    -4     0    -2    -4    -2     1     0    -4    -2    -3     4     0    -1    -5
    -2    -2     2     8    -4     0     2    -1    -1    -4    -4    -1    -4    -5    -1     0    -1    -5    -3    -4     5     1    -1    -5
    -1    -4    -2    -4    13    -3    -3    -3    -3    -2    -2    -3    -2    -2    -4    -1    -1    -5    -3    -1    -3    -3    -2    -5
    -1     1     0     0    -3     7     2    -2     1    -3    -2     2     0    -4    -1     0    -1    -1    -1    -3     0     4    -1    -5
    -1     0     0     2    -3     2     6    -3     0    -4    -3     1    -2    -3    -1    -1    -1    -3    -2    -3     1     5    -1    -5
     0    -3     0    -1    -3    -2    -3     8    -2    -4    -4    -2    -3    -4    -2     0    -2    -3    -3    -4    -1    -2    -2    -5
    -2     0     1    -1    -3     1     0    -2    10    -4    -3     0    -1    -1    -2    -1    -2    -3     2    -4     0     0    -1    -5
    -1    -4    -3    -4    -2    -3    -4    -4    -4     5     2    -3     2     0    -3    -3    -1    -3    -1     4    -4    -3    -1    -5
    -2    -3    -4    -4    -2    -2    -3    -4    -3     2     5    -3     3     1    -4    -3    -1    -2    -1     1    -4    -3    -1    -5
    -1     3     0    -1    -3     2     1    -2     0    -3    -3     6    -2    -4    -1     0    -1    -3    -2    -3     0     1    -1    -5
    -1    -2    -2    -4    -2     0    -2    -3    -1     2     3    -2     7     0    -3    -2    -1    -1     0     1    -3    -1    -1    -5
    -3    -3    -4    -5    -2    -4    -3    -4    -1     0     1    -4     0     8    -4    -3    -2     1     4    -1    -4    -4    -2    -5
    -1    -3    -2    -1    -4    -1    -1    -2    -2    -3    -4    -1    -3    -4    10    -1    -1    -4    -3    -3    -2    -1    -2    -5
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Return a BLOSUM matrix with the amino acids in a specific order.

B75 = blosum(75,'Order','CSTPAGNDEQHRKMILVFYW')
B75 = 20×20

     9    -1    -1    -4    -1    -3    -3    -4    -5    -3    -4    -4    -4    -2    -1    -2    -1    -2    -3    -3
    -1     5     1    -1     1    -1     0    -1     0     0    -1    -1     0    -2    -3    -3    -2    -3    -2    -3
    -1     1     5    -1     0    -2     0    -1    -1    -1    -2    -1    -1    -1    -1    -2     0    -2    -2    -3
    -4    -1    -1     8    -1    -3    -3    -2    -1    -2    -2    -2    -1    -3    -3    -3    -3    -4    -4    -5
    -1     1     0    -1     4     0    -2    -2    -1    -1    -2    -2    -1    -1    -2    -2     0    -3    -2    -3
    -3    -1    -2    -3     0     6    -1    -2    -3    -2    -2    -3    -2    -3    -5    -4    -4    -4    -4    -3
    -3     0     0    -3    -2    -1     6     1    -1     0     0    -1     0    -3    -4    -4    -3    -4    -3    -4
    -4    -1    -1    -2    -2    -2     1     6     1    -1    -1    -2    -1    -4    -4    -4    -4    -4    -4    -5
    -5     0    -1    -1    -1    -3    -1     1     5     2     0     0     1    -2    -4    -4    -3    -4    -3    -4
    -3     0    -1    -2    -1    -2     0    -1     2     6     1     1     1     0    -3    -3    -2    -4    -2    -2
    -4    -1    -2    -2    -2    -2     0    -1     0     1     8     0    -1    -2    -4    -3    -4    -2     2    -2
    -4    -1    -1    -2    -2    -3    -1    -2     0     1     0     6     2    -2    -3    -3    -3    -3    -2    -3
    -4     0    -1    -1    -1    -2     0    -1     1     1    -1     2     5    -2    -3    -3    -3    -4    -2    -4
    -2    -2    -1    -3    -1    -3    -3    -4    -2     0    -2    -2    -2     6     1     2     1     0    -2    -2
    -1    -3    -1    -3    -2    -5    -4    -4    -4    -3    -4    -3    -3     1     4     1     3     0    -2    -3
      ⋮

Input Arguments

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Percent identity, specified as a scalar value from 30 to 90 in increments of 5, 62, or 100.

Data Types: double

Name-Value Arguments

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Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: Matrix = blosum(Identity,Extended=true)

Flag to control the listing of extended amino acid codes, specified as a numeric or logical true (1) or false (0).

Legal amino acid characters that specify the order of amino acids listed in the matrix, specified as a character vector or string scalar. The length of the character vector or string must be 20 or 24.

Output Arguments

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BLOSUM scoring matrix with a specified percent identity, returned as a matrix.

Matrix information, returned as a structure. The structure contains the following fields.

  • Name

  • Scale

  • Entropy

  • ExpectedScore

  • HighestScore

  • LowestScore

  • Order

Version History

Introduced before R2006a

See Also

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