PFASUM {DECIPHER} | R Documentation

## PFASUM Amino Acid Substitution Matrices

### Description

The PFASUM amino acid substitution matrices defined by Keul, F., et al. (2017).

### Usage

    data("PFASUM")

### Format

The format is: num [1:25, 1:25, 1:90] 0.9492 -1.7337 0.2764 1.8153 0.0364 ... - attr(*, "dimnames")=List of 3 ..$ : chr [1:25] "A" "R" "N" "D" ... ..$ : chr [1:25] "A" "R" "N" "D" ... ..$ : chr [1:90] "11" "12" "13" "14" ...

### Details

Substitution matrix values represent the log-odds of observing an aligned pair of amino acids versus the likelihood of finding the pair by chance. The PFASUM substitution matrices are stored as an array named by each sub-matrix's similarity threshold. (See examples section below.) In all cases values are in units of third-bits (log(odds\ ratio)*3/log(2)).

### Source

Keul, F., et al. (2017). PFASUM: a substitution matrix from Pfam structural alignments. BMC Bioinformatics, 18(1), 293.

### Examples

    data(PFASUM)
    PFASUM31 <- PFASUM[,, "31"] # the PFASUM31 matrix
    PFASUM31["A", "R"] # score for A/R pairing

    data(BLOSUM62)
    plot(BLOSUM62[1:20, 1:20], PFASUM31[1:20, 1:20])
    abline(a=0, b=1)

[Package DECIPHER version 2.12.0 Index]