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blosum

Return BLOSUM scoring matrix

Syntax

Matrix = blosum(Identity)
[Matrix, MatrixInfo] = blosum(Identity)

... = blosum(Identity, ...'Extended', ExtendedValue, ...)
... = blosum(Identity, ...'Order', OrderValue, ...)

Input Arguments

Identity

Scalar specifying a percent identity level. Choices are:

  • Values from 30 to 90 in increments of 5

  • 62

  • 100

ExtendedValueControls the listing of extended amino acid codes. Choices are true (default) or false.
OrderValueCharacter vector of legal amino acid characters that specifies the order amino acids are listed in the matrix. The length of the character vector must be 20 or 24.

Output Arguments

MatrixBLOSUM (Blocks Substitution Matrix) scoring matrix with a specified percent identity.
MatrixInfo

Structure of information about Matrix containing the following fields:

  • Name

  • Scale

  • Entropy

  • ExpectedScore

  • HighestScore

  • LowestScore

  • Order

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 *.

A R N D C Q E G H I L K M F P S T W Y V B Z X *

[Matrix, MatrixInfo] = blosum(Identity) returns MatrixInfo, a structure of information about Matrix, a BLOSUM matrix. MatrixInfo contains the following fields:

  • Name

  • Scale

  • Entropy

  • ExpectedScore

  • HighestScore

  • LowestScore

  • Order

... = blosum(Identity, ...'PropertyName', PropertyValue, ...) calls blosum with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:


... = blosum(Identity, ...'Extended', ExtendedValue, ...)
controls the listing of extended amino acid codes. Choices are true (default) or false. If ExtendedValue is false, returns the scoring matrix for the standard 20 amino acids. Ordering of the output when ExtendedValue is false is

A R N D C Q E G H I L K M F P S T W Y V

... = blosum(Identity, ...'Order', OrderValue, ...) returns a BLOSUM matrix ordered by OrderValue, a character vector of legal amino acid characters that specifies the order amino acids are listed in the matrix. The length of the character vector must be 20 or 24.

Examples

collapse all

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

B50 = blosum(50)
B50 =

  Columns 1 through 13

     5    -2    -1    -2    -1    -1    -1     0    -2    -1    -2    -1    -1
    -2     7    -1    -2    -4     1     0    -3     0    -4    -3     3    -2
    -1    -1     7     2    -2     0     0     0     1    -3    -4     0    -2
    -2    -2     2     8    -4     0     2    -1    -1    -4    -4    -1    -4
    -1    -4    -2    -4    13    -3    -3    -3    -3    -2    -2    -3    -2
    -1     1     0     0    -3     7     2    -2     1    -3    -2     2     0
    -1     0     0     2    -3     2     6    -3     0    -4    -3     1    -2
     0    -3     0    -1    -3    -2    -3     8    -2    -4    -4    -2    -3
    -2     0     1    -1    -3     1     0    -2    10    -4    -3     0    -1
    -1    -4    -3    -4    -2    -3    -4    -4    -4     5     2    -3     2
    -2    -3    -4    -4    -2    -2    -3    -4    -3     2     5    -3     3
    -1     3     0    -1    -3     2     1    -2     0    -3    -3     6    -2
    -1    -2    -2    -4    -2     0    -2    -3    -1     2     3    -2     7
    -3    -3    -4    -5    -2    -4    -3    -4    -1     0     1    -4     0
    -1    -3    -2    -1    -4    -1    -1    -2    -2    -3    -4    -1    -3
     1    -1     1     0    -1     0    -1     0    -1    -3    -3     0    -2
     0    -1     0    -1    -1    -1    -1    -2    -2    -1    -1    -1    -1
    -3    -3    -4    -5    -5    -1    -3    -3    -3    -3    -2    -3    -1
    -2    -1    -2    -3    -3    -1    -2    -3     2    -1    -1    -2     0
     0    -3    -3    -4    -1    -3    -3    -4    -4     4     1    -3     1
    -2    -1     4     5    -3     0     1    -1     0    -4    -4     0    -3
    -1     0     0     1    -3     4     5    -2     0    -3    -3     1    -1
    -1    -1    -1    -1    -2    -1    -1    -2    -1    -1    -1    -1    -1
    -5    -5    -5    -5    -5    -5    -5    -5    -5    -5    -5    -5    -5

  Columns 14 through 24

    -3    -1     1     0    -3    -2     0    -2    -1    -1    -5
    -3    -3    -1    -1    -3    -1    -3    -1     0    -1    -5
    -4    -2     1     0    -4    -2    -3     4     0    -1    -5
    -5    -1     0    -1    -5    -3    -4     5     1    -1    -5
    -2    -4    -1    -1    -5    -3    -1    -3    -3    -2    -5
    -4    -1     0    -1    -1    -1    -3     0     4    -1    -5
    -3    -1    -1    -1    -3    -2    -3     1     5    -1    -5
    -4    -2     0    -2    -3    -3    -4    -1    -2    -2    -5
    -1    -2    -1    -2    -3     2    -4     0     0    -1    -5
     0    -3    -3    -1    -3    -1     4    -4    -3    -1    -5
     1    -4    -3    -1    -2    -1     1    -4    -3    -1    -5
    -4    -1     0    -1    -3    -2    -3     0     1    -1    -5
     0    -3    -2    -1    -1     0     1    -3    -1    -1    -5
     8    -4    -3    -2     1     4    -1    -4    -4    -2    -5
    -4    10    -1    -1    -4    -3    -3    -2    -1    -2    -5
    -3    -1     5     2    -4    -2    -2     0     0    -1    -5
    -2    -1     2     5    -3    -2     0     0    -1     0    -5
     1    -4    -4    -3    15     2    -3    -5    -2    -3    -5
     4    -3    -2    -2     2     8    -1    -3    -2    -1    -5
    -1    -3    -2     0    -3    -1     5    -4    -3    -1    -5
    -4    -2     0     0    -5    -3    -4     5     2    -1    -5
    -4    -1     0    -1    -2    -2    -3     2     5    -1    -5
    -2    -2    -1     0    -3    -1    -1    -1    -1    -1    -5
    -5    -5    -5    -5    -5    -5    -5    -5    -5    -5     1

Return a BLOSUM matrix with the amino acids in a specific order.

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

  Columns 1 through 13

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

  Columns 14 through 20

    -2    -1    -2    -1    -2    -3    -3
    -2    -3    -3    -2    -3    -2    -3
    -1    -1    -2     0    -2    -2    -3
    -3    -3    -3    -3    -4    -4    -5
    -1    -2    -2     0    -3    -2    -3
    -3    -5    -4    -4    -4    -4    -3
    -3    -4    -4    -3    -4    -3    -4
    -4    -4    -4    -4    -4    -4    -5
    -2    -4    -4    -3    -4    -3    -4
     0    -3    -3    -2    -4    -2    -2
    -2    -4    -3    -4    -2     2    -2
    -2    -3    -3    -3    -3    -2    -3
    -2    -3    -3    -3    -4    -2    -4
     6     1     2     1     0    -2    -2
     1     4     1     3     0    -2    -3
     2     1     4     1     0    -1    -2
     1     3     1     4    -1    -2    -3
     0     0     0    -1     6     3     1
    -2    -2    -1    -2     3     7     2
    -2    -3    -2    -3     1     2    11

Introduced before R2006a

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