setting up a BLAT server locally

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ryan_m's picture
setting up a BLAT server locally

There have been times I have needed to BLAT large numbers of ESTs against the genome. At one point UCSC began to limit my queries because I was bogging down their server. If you need to run many BLAT jobs in an automated fashion, try setting up a local BLAT server. The link below is a protocol for doing this, including how you can replicate the scores and "i'm feeling lucky" functionality of the UCSC BLAT page.

BLAT server