how to pairwise BLAST very short sequences?

Philipp Pagel philipp.pagel at
Fri Apr 23 08:23:09 EST 2004

Christoph Bock <usenet at> wrote:

> 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

BLAST is probably not a good choice for this application. I would
recommend to use optimal global alignment (Needleman-Wunsch). You could
use the tool 'needle' from the EMBOSS package, for example.


Dr. Philipp Pagel                           Tel.  +49-89-3187-3675
Institute for Bioinformatics / MIPS         Fax.  +49-89-3187-3585
GSF - German National Research Center for Environment and Health
Email: p.pagel AT gsf . de

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