bgafun (version 1.34.0)

BGAfun: BGAfun A method to identify specifity determining residues in protein families

Description

This Package combines between group analysis with sequence alignments to identify specifity determining residues in protein families

References

Wallace, I.M. and Higgins, D.G. (2007) Supervised multivariate analysis of sequence groups to identify specificity determining residues, BMC Bioinformatics, 8, 135.

Examples

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)