>mperr1 at hamon.swmed.edu (Michael Perry) wrote:
>>> >Chris,
> >Sounds like a job for blastx. Point your browser to the NCBI BLAST
> >web page at http://www.ncbi.nlm.nih.gov/BLAST/ and check out the
> >following programs:
>> >blastx: compares a nucleotide query sequence translated in all
> >reading frames against a protein sequence database
>> >tblastx: compares the six-frame translations of a nucleotide query
> >sequence against the six-frame translations of a nucleotide sequence
> >database.
> From ckafer at iastate.edu Wed Oct 2 00:48:50 1996
> Thanks for the reply but I tried that first. What it appears to do is
> compare the entire sequence (as if it were a single ORF) in all 6
> frames. What I would like to do is have it blast the real ORFs >30
> amino acids individually. When I blast them manually, it brings back
> different hits than a blastx search of the entire sequence.
>> As an example, when I blast one of the 200 aa ORFs it returns an EST
> clone. When I blast the entire sequence, of which this ORF is just a
> part, it doesnt show up. Hopefully I explained that clearly!
>> Any other ideas would be appreciated!
Chris,
If I understand correctly, what you want is "tblastn vs est"?
TBLASTN takes a protein query sequence and compares it to the
translation of the EST in 3 or 6 frames (6 is the default).
Is that what you want?
A summary of the various ways of using blast is available
(blatent self citation to follow) from:
http://www.cshl.org:80/books/g_a/bk1ch7/
cheers,
f.
--
| B.F. Francis Ouellette
| GenBank
||francis at ncbi.nlm.nih.gov
