pam

Return Point Accepted Mutation (PAM) scoring matrix

Syntax

ScoringMatrix = pam(N)

[ScoringMatrix,MatrixInfo] = pam(N)

pam(N,Name=Value)

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.

pam(N,Name=Value) specifies additional options using one or more name-value arguments.

Examples

Return the PAM50 Matrix

Use the pam function to 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');

Input Arguments

N — Specification of PAM scoring matrix

10 | 20 | 30 | 40 | 50 | 60 | ... | 470 | 480 | 490 | 500

Specification of PAM scoring matrix to return, represented as an integer.

N accepts integer values starting from 10, and ending at 500 in increments of 10, only. Hence, 270 is a valid input, but not 275.

Tip

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

Example: 450

Data Types: integer

Name-Value Arguments

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: pam(10,Extended=true) returns ambiguous characters: B,Z,X, and the stop character *.

Extended — Flag to return ambiguous characters

false or 0 (default) | true or 1

Flag to return of ambiguous characters: B, Z, and X, and the stop character *, in addition to the 20 standard amino acid characters, specified as a numeric or logical true (1) or false (0).

Data Types: logical

Order — Order of amino acids in scoring matrix

"ARNDCQEGHILKMFPSTWYVBZX*" (default) | character vector | string scalar | ...

Order of amino acids in the scoring matrix, specified as a character vector or string scalar. The input string must be of length 20 at least, with each member of the string representing each of the standard 20 amino acids.

If Order does not contain the ambiguous characters B,Z, X, or *, then these characters are not returned.

You can rearrange the input string in any order, provided the standard 20 amino acids are present.

Example: "QEGCRANDHILKMFPSTWYV"

Data Types: char | string

Output Arguments

ScoringMatrix — PAMN scoring matrix for amino acid sequences

numeric array

PAMN scoring matrix for amino acid sequences, returned as an array of integer values.

MatrixInfo — Information about PAMN matrix

structure

Information about PAMN matrix, returned as a structure. These are the fields of the structure: Name, Scale, Entropy, ExpectedScore, LowestScore, HighestScore, and Order.

For example, PAM50 scoring matrix has the following values.

struct with fields:

             Name: 'PAM50'
            Scale: 0.5000
          Entropy: 2
    ExpectedScore: -3.7000
      LowestScore: -13
     HighestScore: 13
            Order: 'ARNDCQEGHILKMFPSTWYVBZX*'

Version History

Introduced before R2006a