| Bioinformatics Toolbox | |
Return a PAM scoring matrix
ScoringMatrix = pam(N, 'PropertyName', PropertyValue) [ScoringMatirx, MatrixInfo] = pam(N) ScoringMatrix = pam(..., 'Extended', ExtendedValue) ScoringMatrix = pam(..., 'Order', 'OrderValue')
N | Enter values 10:10:500. 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 *. Entering a larger value for N to allow sequence alignments with larger evolutionary distances. |
| Extended | Property to add ambiguous characters to the scoring matrix. Enter either true or false. Default is false. |
| Order | Property to control the order of amino acids in the scoring matrix. Enter a string with at least the 20 standard amino acids. |
ScoringMatrix = pam(N, 'PropertyName', PropertyValue) returns a PAM 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.
B = pam(..., 'Extended', 'ExtendedValue') if Extended is true, returns a scoring matrix with the 20 amino acid characters, the ambiguous characters, and stop character (B, Z, X, *), . If Extended is false, only the standard 20 amino acids are included in the matrix.
B = pam(..., 'Order', 'OrderString') returns a PAM matrix ordered by the amino acid sequence in Order. If Order 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.
Get the PAM matrix with N = 50.
PAM50 = pam(50) PAM250 = pam(250,'Order','CSTPAGNDEQHRKMILVFYW')
Bioinformatics Toolbox functions blosum, dayhoff, gonnet, nwalign, swalign
| | palindromes | pdbdistplot | |
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