[Genome] Blat 35-mer perfect matches

[Ann Zweig]

Hello Derek,

	The -minMatch=N sets the number of tile matches.  The default is 2 for 
nucleotide, 1 for protein.  This is the number of contiguous tile hits necessary 
to seed an alignment attempt.  Setting it higher is probably not good for 
sensitivity.

	Perhaps you should try the -minScore parameter, as well as setting the -stepSize=5.

	After BLATting, try using the pslCDnaFilter program to filter the PSLs (start 
with these parameters: pslCDnaFilter -minAlnSize-35 -minID=1 -minCover=1).

	This should give you a place to start -- you'll have to tweak the parameters to 
get the exact output you're looking for.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


Derek Chiang wrote:
> What parameter settings on the standalone blat would you recommend to 
> find perfect sequence matches of 35 bases in the human genome?  I've 
> tried the parameter settings of -minMatch=3 -minIdentity=100 but noticed 
> that some query sequences lacked any hits.  I assume that tiles with low 
> complexity are filtered out, thus failing the -minMatch requirement.
> 
> Thanks,
> Derek
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