W3 interface to search SwissPROT with two or more peptide sequences at once

Jonathan Epstein Jonathan_Epstein at nih.gov
Mon Jul 6 10:23:23 EST 1998

I'm not sure if this will help you, but you may want to try
ProteinProspector, since you are working with trypsin digests:


- Jonathan

Uwe Baumert wrote:
> Hi,
> I'm looking for an W3 interface to SwissPROT that allows us to search with
> two or more peptide sequences (12-18 aa). The peptides derived from
> trypsin digestions. Additional information that can be provided are pI and
> MW of the undigested protein. All on-line tools I looked so far (starting
> with the Tools page at expasy) need at least one sequence and/or pI and/or
> MW and/or several MS/MS or MALDI data entries and/or sequence tags. Since
> the genome of "our working object" is not subject of a genome project, we
> can only look for homology.
> Each peptide alone gives several hits (about 60 % homology) using FASTA
> but no hits using BLAST.
> Thank you in advance,
> Uwe Baumert
> --
> Institut für Allgemeine Zoologie und Genetik
> Westf. Wilhelms-Universität
> Schloßplatz 5                               Fax : +49 251 83-24723
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