BGAfun {bgafun} | R Documentation |
This Package combines between group analysis with sequence alignments to identify specifity determining residues in protein families
Iain Wallace <iain.wallace@ucd.ie>
Wallace, I.M. and Higgins, D.G. (2007) Supervised multivariate analysis of sequence groups to identify specificity determining residues, BMC Bioinformatics, 8, 135.
library(bgafun) #read in alignment LDH <- read.alignment(file = system.file("sequences/LDH-MDH-PF00056.fasta", package = "bgafun"), format = "fasta") #Assign into groups LDH.amino=convert_aln_amino(LDH) LDH.groups=rownames(LDH.amino) LDH.groups[grep("LDH",LDH.groups)]="LDH" LDH.groups[grep("MDH",LDH.groups)]="MDH" LDH.groups=as.factor(LDH.groups) #Convert to Amino Acid matrix (or Amino Acid properties matrix) LDH.amino.gapless=remove_gaps_groups(LDH.amino,LDH.groups) #Add Psuedo counts LDH.pseudo=LDH.amino.gapless+1 LDH.binary.bga=bga(t(LDH.pseudo),LDH.groups) plot(LDH.binary.bga)