how to pairwise BLAST very short sequences?
James D. Veale
jdveale at TheWorld.com
Thu Apr 22 13:03:45 EST 2004
This is well outside my field, if a simple 'longest common
subsequence' comparison of the two sequences is of any value,
I may be able to help.
where the asterisk's indicate changes. You could add a handful
of allowable substitutions in the comparison. There wouldn't
be any scoring as I understand it, but you could get the number
of deleted, matching, and inserted letters.
No doubt there's a better tool in your field, but feel free to email me
if you don't have any luck.
Jim Veale - jdveale at world.std.com
usenet at christoph-bock.de (Christoph Bock) writes:
>I tried to use NCBI BLAST to estimate the evolutionary distance
>between very short local protein sequence segments in homologous
>proteins with high sequence identity. e.g. KIYKDTEGY against KIKNTEGY
>However, bl2seq constantly fails to come up with an alignment or even
>crashes for those very short sequences. Which other alignment tool
>could I use in order to get score that are comparable to BLAST (e.g.
>As far as I saw, FASTA does not have a sequence-against-sequence mode,
>Thanks for your help,
> Christoph Bock
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