isen at molbio.mgh.harvard.edu (Thomas Isenbarger) 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?
You write a simple DP program that does ends free alignment (ie no gap
penalty for gaps extended from the ends). However, I don't know any
program in the public domain does this. I have a simple Smith-Waterman
program that can be modified to do this in a day. I may do it
eventually but no one is paying me to do it, so there isn't any
urgency here. ;)