[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
More information about the Genome
mailing list