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. doi:10.1093/bioinformatics/btt694.

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(DECIPHER)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: RSQLite
Loading required package: DBI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DECIPHER/MIQS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MIQS
> ### Title: MIQS Amino Acid Substitution Matrix
> ### Aliases: MIQS
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(MIQS)
> MIQS["A", "R"] # score for A/R pairing
[1] -1.3
> 
> data(BLOSUM62)
> plot(BLOSUM62[1:20, 1:20], MIQS[1:20, 1:20])
> abline(a=0, b=1)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>