[Genome] batch queries to BLAT

[Rachel Harte]

Hello Douglas,

There are two ways that you could do this:

1) Download Blat and use it locally. There is a version for use with
Windows. Please go to this link for details on obtaining the downloads:

http://genome.ucsc.edu/FAQ/FAQblat#blat3

Blat is free for academic, non-profit and personal use.

2) I have a blatBot.pl script which will submit sequences from a file in
batches of 25. There is another script that will parse the resulting HTML
file. The scripts may be downloaded from:

http://genomewiki.cse.ucsc.edu/index.php/Blat_Scripts

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Sun, 21 Jan 2007, Douglas D. Rhoads wrote:

> I need to run 3000 sequences against a genome to find the best position
> and score for each sequence.  I am limited to 25 sequences through the
> web site and eventually you trigger the nag about traffic from my IP.  Any
> suggestions about how to proceed would be appreciated.  Do I need to
> download the assembly and then set up a BLAT locally?  Can I do that in
> Windows?
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