short sequence matching

Thomas Isenbarger isen at molbio.mgh.harvard.edu
Sat Feb 8 17:28:52 EST 2003


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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