[Genome] batch query

[Archana Thakkapallayil]

Hello Mathias,

There are 2 ways that you could do this:

1) You can download the Blat program and install it locally to run Blat 
alignments. It is free for personal,academic and non-profit institution 
use. Here is a link to information about downloading Blat:

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

This link tells you how to replicate the parameters used in the 
web-based Blat:

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

2) 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 and 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

Also, please see this previously answered mail list question that gives 
information on filtering out the best hit from the output:

http://www.cse.ucsc.edu/pipermail/genome/2006-March/009918.html

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

Regards,

Archana
UCSC Genome Bioinformatics Group


Mathias Ehrich wrote:
> Dear Genome Browser Team,
>
> I'm would like to blast 600+ sequences. I tried to open several tab's in
> Firefox, but the BLAT site suggests writing to you to inquire more
> efficient ways of doing this. Most of the sequences should be a close to
> perfect match, so that I really only need the first entry in the score
> sorted list. I also have MYSQL connection to the genome browser, but I
> couldn't figure out how to do BLAT searches.
>
> Please help me out of this dilemma. 
>
> Thanks.
>
> Mathias Ehrich
>
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