[Genome] Automating web BLAT

[Rachel Harte]

Hello Yuval,

I have a perl script that allows you to submit a file of sequences to our
BLAT server. It obeys our site's rules for Blat, submitting only 25 sequences
and pausing for 2 minutes between submissions.
The script (BlatBot.pl) may be downloaded from here:
http://genomewiki.cse.ucsc.edu/index.php/Blat_Scripts

The output is HTML so the parseBlatOutput.pl script may be used remove the
HTML.

Please let me know if you have any questions or find any problems.

Rachel

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


On Thu, 4 Jan 2007, Yuval Itan wrote:

> Hello,
>
> I have a few hundred cDNA sequences that I need to BLAT against the
> human, chimp and macaque genome. I can't do it locally because these
> tasks require huge memory (2GB of my computer is not enough).
> Doing it manually through your web interface will require many hours of
> very tedious work, due to the 25 sequences limitation.
> I was wondering if you know of a way to automatically perform this task
> using your (or other) web interface.
>
> Thanks,
>
> Yuval
>
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