pam

Return Point Accepted Mutation (PAM) scoring matrix

Syntax

ScoringMatrix = pam(N)
[ScoringMatrix, MatrixInfo] = pam(N)

... = pam(N, ...'Extended', ExtendedValue, ...)
... = pam(N, ...'Order', OrderValue, ...)

Arguments

N

Integer specifying the PAM scoring matrix to return. Choices are 10:10:500.

    Tip   Entering a larger value for N allows for sequence alignments with larger evolutionary distances.

ExtendedValue

Controls the return of the ambiguous characters (B, Z, and X), and the stop character (*), in addition to the 20 standard amino acid characters. Choices are true or false (default).

OrderValue

String that controls the order of amino acids in the scoring matrix. Choices are a string with at least the 20 standard amino acids. The default order of the output is A R N D C Q E G H I L K M F P S T W Y V B Z X *. If OrderValue does not contain the characters B, Z, X, and *, then these characters are not returned.

Description

ScoringMatrix = pam(N) returns the PAMN scoring matrix for amino acid sequences.

[ScoringMatrix, MatrixInfo] = pam(N) returns a structure with information about the PAM matrix. The fields in the structure are Name, Scale, Entropy, Expected, and Order.

... = pam(N, ...'PropertyName', PropertyValue, ...) calls pam 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:


... = pam(N, ...'Extended', ExtendedValue, ...)
controls the return of the ambiguous characters (B, Z, and X), and the stop character (*), in addition to the 20 standard amino acid characters. Choices are true or false (default).

... = pam(N, ...'Order', OrderValue, ...) controls the order of amino acids in the returned scoring matrix. Choices are a string with at least the 20 standard amino acids. The default ordering of the output is A R N D C Q E G H I L K M F P S T W Y V B Z X *. If OrderValue does not contain the extended characters B, Z, X, and *, then these characters are not returned.

PAM50 substitution matrix in 1/2 bit units, Expected score = -3.70, Entropy = 2.00 bits, Lowest score = -13, Highest score = 13.

PAM250 substitution matrix in 1/3 bit units, Expected score = -0.844, Entropy = 0.354 bits, Lowest score = -8, Highest score = 17.

Examples

Return the PAM50 matrix.

PAM50 = pam(50)

Return the PAM250 matrix and specify the order of amino acids in the matrix.

PAM250 = pam(250,'Order','CSTPAGNDEQHRKMILVFYW')
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