[Bioperl-l] query in BLAT usage

neeti somaiya neetisomaiya at gmail.com
Tue Nov 29 05:35:19 EST 2005


I am using BLAT in a project. I have read that each blat run is typically
done against a single chromosome, but with a large number of query
I have to BLAT gene sequences against a chromosomes sequence.
Can I have sequences of all the genes in FASTA format, one following the
other, in a single .fa file as the query file and BLAT it against a .fa file
as the database, which has the sequence of the chromosome in FASTA format?

Also, running a BLAT of a 27025 bases gene, against a chromosome of size
57701691 bases took 70 mins to run (on a Linux machine). Is there any means
of increasing the speed of the BLAT run?

Thanks and Regards,

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