Seq Search w/ Multiple Small Frag.

mathog at seqaxp.bio.caltech.edu mathog at seqaxp.bio.caltech.edu
Fri Dec 19 18:38:59 EST 1997


In article <67ebvo$rob$1 at magnolia.pe.net>, williams at magnolia.pe.net (Alan Williams) writes:
>I have sequence information for six peptide fragments from a trysin
>digest.  Are there any programs that will search the databases using
>the info in the six fragments to find significant matches.

Yes, BLAST.

You have to mess about quite a bit to do this though.  For one thing, you
have to use "-sort_by_total_score".  You also have to set the cutoff for
the individual HSPs very low, signify gaps between the peptides with
"-", and set the cutoff for the cumulative score to be something reasonable
and considerably higher than the individual HSP cutoff.

All that being said, I recall that this function has been broken from time 
to time, and I have not run it myself in years.  If you can't make it work,
email them and see if it is still supported. 

Regards,

David Mathog
mathog at seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 




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