aa.index {bio3d} | R Documentation |
A collection of published indices, or scales, of numerous physicochemical and biological properties of the 20 standard aminoacids (Release 9.1, August 2006).
data(aa.index)
A list of 544 named indeces each with the following components:
‘AAIndex’ was obtained from:
ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1
For a description of the ‘AAindex’ database see:
http://www.genome.jp/aaindex/.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
‘AAIndex’ is the work of Kanehisa and co-workers:
Kawashima and Kanehisa (2000) Nucleic Acids Res. 28, 374;
Tomii and Kanehisa (1996) Protein Eng. 9, 27–36;
Nakai, Kidera and Kanehisa (1988) Protein Eng. 2, 93–100.
## Load AAindex data data(aa.index) ## Find all indeces described as "volume" ind <- which(sapply(aa.index, function(x) length(grep("volume", x$D, ignore.case=TRUE)) != 0)) ## find all indeces with author "Kyte" ind <- which(sapply(aa.index, function(x) length(grep("Kyte", x$A)) != 0)) ## examine the index aa.index[[ind]]$I ## find indeces which correlate with it all.ind <- names(which(Mod(aa.index[[ind]]$C) >= 0.88)) ## examine them all sapply(all.ind, function (x) aa.index[[x]]$I)