Blast search help needed.

francis at NCBI.NLM.NIH.GOV francis at NCBI.NLM.NIH.GOV
Wed Oct 2 00:01:34 EST 1996


> 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   







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