how to pairwise BLAST very short sequences?

Christoph Bock usenet at
Wed Apr 21 22:36:40 EST 2004


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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