BLAST versus BLAT, limit for the length of the query

Richard Williams rdwillia at hgmp.mrc.ac.uk
Mon Jul 8 03:53:55 EST 2002

In article <1eb3f133.0206130406.a971a82 at posting.google.com>,
Andrea <webmaster at bioinformatik.de> wrote:

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

I've used standalone BLAT (downloaded from Jim Kent's site). It's more 
like Megablast than like BLAST itself (though the algorithm is different) 
- it's optimised for matching highly similar sequences, and may miss 
the more divergent sequences and shorter alignments that BLAST detects. 
For tasks like matching a few hundred ESTs to a genome, I've found that 
BLAT is much faster than NCBI BLAST, but gives comparable alignments that 
are easier to parse (you get a nice tabular output - the sequences 
themselves aren't shown). Megablast (included in the NCBI BLAST 
distribution) may also have these advantages, but I haven't done a direct 


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