short sequence matching

Yee Man Chan ymc at yahoo.com
Mon Feb 17 05:27:04 EST 2003

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?
> Thanks
> ---

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. ;)

Good luck!
Yee Man

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