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

Author(s)

Iain Wallace <iain.wallace@ucd.ie>

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(bgafun)
Loading required package: made4
Loading required package: ade4
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: scatterplot3d
Loading required package: seqinr
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/bgafun/bgafun.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BGAfun
> ### Title: BGAfun A method to identify specifity determining residues in
> ###   protein families
> ### Aliases: bgafun
> ### Keywords: package
> 
> ### ** 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)
 [1]   61  161  210  253  291  391  807  820 1014 1224 1376 1562 1575 1582 1673
[16] 1731 2403 2404 2510 2558 2616 2675 2788
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>