Urgent request: combined peptide database search

Vladimir Morozov morozov at lion-ag.de
Thu Aug 12 06:59:43 EST 1999


Christian Götting wrote:

> How can I search for matches within the EMBL databases (nr and est) with
> a combination of aminoacid sequences ?
> I do have the aminoacid sequences of 3 peptides (too short for a search
> on its own) and want to do a combined search. Can anyone tell me what

I thing it is not goof idea to combine peptides from different genes.  In
the case I would suggest to apply TFastx/TFasty (i.e
.http://www2.ebi.ac.uk/fasta3/newfasta3.html).
As far I remember there is no mimimal lenth for query in FASTA. It seems be
more sensitive than BLAST against DNA (particularly EST) database because a
frame shift is allowed.


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