MIQS: MIQS Amino Acid Substitution Matrix

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

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)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: RSQLite
[1] -1.3

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.