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

[Philippe DESSEN]

Hello,

numerous versions of fasta programs could solve your problem
See the site of William Pearson at Virginia University :

http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml

You can use either the server or download the programs 

best regards

Philippe Dessen
IGR, Villejuif, France



Le 4 janv. 2013 à 16:20, Juliet Hannah a écrit :

> 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)
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor