Is it possible to do charge and/or hydrophobicity analysis of multiple aligned sequences in Bio3d?

[Former user]

No description provided.

[Barry Grant]

Yes you can look at over 500 published physicochemical and biological property scales using the aa.index data and bio3d.

For example below we examine the hydrophobicity of aligned sequences (using the Kyte-Doolittle Hydropathy index). For simple net charge you could use the scale from Klein et al., (1984) i.e. aa.index[["KLEP840101"]] See http://www.genome.jp/aaindex/ for more details on available scales/indexes

library(bio3d)

## Read an example alignment
file <- system.file("examples/hivp_xray.fa",package="bio3d")
aln <- read.fasta( file )

## Load AAindex data
data(aa.index)

## Find Kyte-Doolittle Hydropathy index (Kyte-Doolittle, 1982)
##  grep for author "Kyte" to loacte this entry 
ind <- which(sapply(aa.index, function(x) length(grep("Kyte", x$A)) != 0))

## Store the 'index' values for the 20 standard amino acids
index <- aa.index[[ind]]$I

# print these values
index

## Plot vector of hydropathy vales for the first sequence
plot( index[ aln$ali[1,] ], typ="l", 
     xlab="Alignment position", ylab="Hydropathy (Kyte-Doolittle, 1982)")

## Store values for all alignment sequences
hydro.aln <- NULL
for(i in 1:nrow(aln$ali)) {
  hydro.aln <- rbind(hydro.aln, index[ aln$ali[i,] ])
}

## Plot mean value per alignment position
hydro.ave <- apply(hydro.aln,2,mean,na.rm=TRUE)
plot(hydro.ave, typ="o",
     xlab="Alignment position", ylab="Hydropathy (Kyte-Doolittle, 1982)")

Looking at larger alignments can be helpful, e.g.

## Example 2. Look at a larger PFAM alignment and remove gap positions from plot
file <- "http://pfam.xfam.org/family/PF00503/alignment/seed/format?format=fasta"
aln <- read.fasta( file )

hydro.aln <- NULL
for(i in 1:nrow(aln$ali)) {
  hydro.aln <- rbind(hydro.aln, index[ aln$ali[i,] ])
}

hydro.ave <- apply(hydro.aln,2,mean,na.rm=TRUE)
ngaps <- gap.inspect(aln)$f.inds

plot(hydro.ave[ngaps], typ="o")