[BioC] BLAST in R

[January Weiner]

Dear Zoha,

I think the simplest thing to do is to invoke the command line blast
from R, using the option -m 8 to get tabular output that can be
automatically parsed by read.table. Example:

myPipe <- pipe( "blastall -p blastp -i text.fasta -d data.fasta" )
results <- read.table( myPipe )
colnames( blastResults ) <- c( "QueryID",  "SubjectID", "Perc.Ident",
"Alignment.Length", "Mismatches", "Gap.Openings", "Q.start", "Q.end",
"S.start", "S.end", "E", "Bits" )

However, that way you will not get the actual alignments.

Cheers,

j.

On Mon, Jun 6, 2011 at 4:49 PM, Zoha Moztarzadeh <zoha_mozt at yahoo.com> wrote:
> Hello bioconductor group,
>
> I have a FASTA sequences (without ID) and would like to find the homolge sequneces with BLAST.
> How can I do this in R explain me haw to do multiple sequence alignment with them.
>
> Thanks in advance,
>
> Zoha
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>
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-- 
-------- Dr. January Weiner 3 --------------------------------------
Max Planck Institute for Infection Biology
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