short sequence matching

Geronimo user at server.com
Wed Feb 19 04:46:19 EST 2003


Set the E parameter in BLAST to 1000 or higher. It works, believe me -- this
is how some of the error-prone DNA polymerases were discovered. :)


"Thomas Isenbarger" <isen at molbio.mgh.harvard.edu> wrote in message
news:isen-5F54BB.17281208022003 at plato.harvard.edu...
> Can anyone recommend a UNIX program (for Mac OS X variety) or how to
> tweak the standalone BLAST program to do this. . .
>
> I want to search databases with short DNA sequences (15-50 nt) and look
> for exact matches or a few mismatches.  I want it to use the whole short
> sequence to do the matching and not just a part of it.  I suppose a
> program that looks for PCR primers might work for this, but those
> probably ask for salt concentrations, GC richness, etc.
>
> Any help?
>
> Thanks
> ---
>





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