[R] Probing a protein sequence alignment in R

[Boris Steipe]

One way would be to use the biostrings and msa packages from bioconductor.

Use AAStringSet() to collect your sequences, and (e.g.) msaMuscle() to align them. Then use BStringset() to extract the subrange you need, and e.g. table to look at the distributions...

table(BStringSet(<output-of-msaMuscle>, start=50, width=1))

Working with Bioconductor S4 objects can be a bit salty, so mail again if you need more explicit sample code.

Cheers,
Boris


On Nov 24, 2015, at 12:04 PM, debra ragland via R-help <r-help at r-project.org> wrote:

> I have 15 protein sequences of 99 amino acids each. After doing some looking around I have found that there are several ways you can read sequences into R and do pairwise or multiple alignments. I, however, do not know how to probe changes at specific positions. For instance, I would like to know the best way to align a standard sequence with one(1) or several mutant sequences and probe each amino acid position that does not match the standard sequence. In other words seq1 = "standard amino acid seq" and seq2 = "mutant seq", align these 2 and then have a way to ask R to report whether there is a change at position 10, or 11, or 12 and so on such that R reports(for example) TRUE or FALSE for this question. Where all the sequences that have a reported TRUE for a change at position X can be grouped against those that do not have a change at this position.I'm not even sure that R is the best way to do this, but it's the only language I'm somewhat familiar with.I hope this makes !
> sense. Any help will be appreciated.
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.