MIQS {DECIPHER} | R Documentation

## MIQS Amino Acid Substitution Matrix

### Description

The MIQS amino acid substitution matrix defined by Yamada & Tomii (2014).

### Usage

    data("MIQS")

### Format

The format is: num [1:25, 1:25] 3.2 -1.3 -0.4 -0.4 1.5 -0.2 -0.4 0.4 -1.2 -1.3 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:25] "A" "R" "N" "D" ... ..$ : chr [1:25] "A" "R" "N" "D" ...

### 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. Values in the MIQS matrix are in units of third-bits (log(odds\ ratio)*3/log(2)).

### Source

Yamada, K., & Tomii, K. (2014). Revisiting amino acid substitution matrices for identifying distantly related proteins. Bioinformatics, 30(3), 317-325.

### Examples

    data(MIQS)
    MIQS["A", "R"] # score for A/R pairing

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

[Package DECIPHER version 2.20.0 Index]