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.
KIYKDTEGY
* *
KIKNTEGY
*
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.comusenet 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.
>using BLOSUM62)?
>As far as I saw, FASTA does not have a sequence-against-sequence mode,
>only sequence-against-database?
>Thanks for your help,
> Christoph Bock