BLATBOT

localにBLATを設置できない（メモリを十分に積んだマシンがない）質問者に対して、UCSCの中の人が紹介した（webの）BLATに対してクエリーを投げるスクリプト。
UCSC製だから、ルール通りなのがgoodなところか。

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

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