BLAST versus BLAT, limit for the length of the query

Kevin Karplus karplus at
Wed Jun 19 03:36:54 EST 2002

>> 2. Has anyone here experience with the new "Blast" called Blat?
>> Do you think it will be faster than BLAST?
>> Are the results comparable?

BLAT is much faster than BLAST when doing many DNA-based searches in a
big genome like the human genome, but it will probably miss more
remote similarities than BLAST, as it has been mainly tuned for
mouse-human genomic distances.  There are parameters that can be
adjusted to make it more sensitive but slower.

BLAT indexes the genome, which is fairly expensive, so is only a win
if you plan to do many searches. 

Kevin Karplus 	karplus at
Professor of Computer Engineering, University of California, Santa Cruz
Undergraduate Director, Bioinformatics
Affiliations for identification only.

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