[Genome] BLAT Search Question

[Emmanuel Kamberov]

Hi, we are trying to create a custom annotation track from BLAT search
output.  We have a few hundred short genomic DNA sequences (80-150 bp
long).  How many sequences can be processed in one batch ?  Is there a
way to filter only the highest scorring match for each sequence  when
creating a PSL output file ?  
 
Thanks,
 
Emmanuel Kamberov
 
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Emmanuel Kamberov, Ph.D.
Senior Research Scientist
Rubicon Genomics, Inc.
4370 Varsity Drive,
Ann Arbor, MI 48103
Office:    734-677-2894
Mobile:   734-274-1102
kamberov at rubicongenomics.com <mailto:kamberov at rubicongenomics.com> 
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