substitution {aphid}R Documentation

Substitution matrices.

Description

A dataset containing several popular substitution scoring matrices for DNA and amino acids.

Usage

substitution

Format

A list of 71 matrices, most of which have 24 rows and 24 columns corresponding to the 20-letter amino acid alphabet plus the ambiguity codes B, Z, X and *:

PAM

the PAM matrices from PAM10 to PAM500.

BLOSUM

the BLOSUM matrices from BLOSUM30 to BLOSUM100.

others

also included are the DAYHOFF, GONNET, IDENTITY and MATCH substitution matrices for amino acids, and the NUC.4.2 and NUC.4.4 substitution matrices for DNA.

Source

ftp://ftp.ncbi.nih.gov/blast/matrices/


[Package aphid version 1.3.3 Index]