[BioC] strategy to match/align peptide sequence to protein

[Hervé Pagès]

Hi Juliet,

Yes matchPattern() should work. Did you run into any problems?

However note that by default, matchPattern() will do exact matching.
If you want to allow for some mismatches and/or indels, you can use
the 'max.mismatch' and 'with.indels' args. See ?matchPattern for
the details.

And if you want to use the full power of the Smith-Waterman algo,
you can use pairwiseAlignment(), which lets you do global, global-local,
and local-local alignments, with the substitution matrix and gap
penalties of your choice. See ?pairwiseAlignment for the details.
There is also a full vignette (PairwiseAlignments) dedicated to this
in the Biostrings package.

I could try to help more if you had more specific questions.

Cheers,
H.


On 01/04/2013 07:20 AM, Juliet Hannah wrote:
> All,
>
> Given a list of small peptide sequences and swissprot identifiers, I
> would like to find out where the
> peptide aligns to the full protein.
>
> The script I am using is below. I am seeking any comments on the
> strategy (are there alternatives,
> is there a better way to align...etc).
>
> Thanks,
>
> Juliet
>
> # given "HEMO_HUMAN"
> # get sequence from biomart
>
> library("biomaRt")
> mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
> seq = getSequence(id="HEMO_HUMAN", type="uniprot_swissprot",
> seqType="peptide", mart = mart)
> show(seq)
>
> library(Biostrings)
>
> # find out where short sequence toFind falls along full protein
>
> toFind <- "ARVLGA"
> matchPattern(toFind,seq$peptide)
>
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-- 
Hervé Pagès

Program in Computational Biology
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