Question about running multiple sequences in BLAT

[Pavel Alexandrovich Vlasov]

Dear UCSC Genome Institute,

I'm currently trying to use BLAT to align a set of sequences to the hg19 genome. However, I have too many sequences in my data set to run them one at a time. 

If I understand correctly, the online BLAT tool can only test one sequence at a time. Is it possible to run multiple sequences another way? Is there a downloadable version of BLAT that can run larger data sets locally?

Sincerely,

Pavel Vlasov,

Columbia University

[Robert Kuhn]

Dear Pavel,

thanks for you interest in the browser and blat. Here is some documentation about using blat.

http://genome.ucsc.edu/FAQ/FAQblat.html

If you have a very large number of sequences (you did not define "too many."  tens?  hundreds? 

thousands?) you may need to use out command-line blat.  You can paste in up to 25 at time into

the web interface as long as each has a name in a fasta header:

> seq1

ATAAACGCTAGCTCGAGA...

> seq2

ATAAGGAAACCTCAGATC...

etc.

best wishes,

    --b0b kuhn

   ucsc genome bioinformatics group

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