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

[Juliet Hannah]

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)