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	Character vector or string that controls the order of amino acids in the scoring matrix. Choices are a character vector or 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 character vector or 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')