how to pairwise BLAST very short sequences?

James D. Veale jdveale at
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

usenet at (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

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