[Genome] batch Blat run

[Ann Zweig]

Hello Michael,

	If you do not want to install a local copy of BLAT, you can use a perl script 
which was created by one of our developers.  This script takes a file of FASTA 
format sequences as input and then submits them to the web-based Blat on the 
UCSC Genome Browser web site. It obeys the site rules for the number of 
frequency of hits i.e. Program-driven use of the Genome Browser software is 
limited to a maximum of one hit every 15 seconds and Blats sequences in batches 
of 25 sequences at a time.  You can find information about the script and a link 
to it, on our wiki site:  http://genomewiki.cse.ucsc.edu/index.php/Blat_Scripts

	Hope this is helpful to you.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Michael Place wrote:
> I would like to run a batch blat job (790 sequences <5000bp).
> What is the best way to do this?  I do not want to download blat and run 
> it locally
> as this is a one time job. 
> 
> Any help is greatly appreciated.
> Thank you,
> 
> Mike Place
> 
> Payseur Lab
> Laboratory of Genetics
> Genetics/Biotechnology 2428
> 425-G Henry Mall
> University of Wisconsin
> Madison, WI 53706
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