[Genome] BLAT short sequence queries ( 12mer to 30mer )

John Major major at cbio.mskcc.org
Fri Oct 6 10:23:34 PDT 2006


Hello-

I have a large amount of 12-30bp sequences which I'd like to find exact 
(or 1 bp mismatch) alignments to the Drosophila genome.  I have a local 
install of BLAT and have played with the parameters, but can't seem to 
return any hits for the shorter sequences (in the 12-15bp range mostly).
I have run the s/w w/out the 11.ooc file, and with  tileSize=8, 
minMatch=2, stepSize=5, but with no luck. 

I see in a post from 2002 that BLAT can't handle sequence searches below 
21bp in length.  Is this still true?
Are there recommended settings to run BLAT on short sequences?

Thanks,
John


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