DECIPHER (version 2.0.2)

MIQS: 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" ...

Source

Yamada, K., & Tomii, K. (2014). Revisiting amino acid substitution matrices for identifying distantly related proteins. Bioinformatics, 30(3), 317-325. doi:10.1093/bioinformatics/btt694.

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 ($log(odds\ ratio)*3/log(2)$).

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)