[Genome] Using web blat

[Rachel Harte]

Hello Wes,

There are two approaches that you could use. Firstly, you can download
Blat and use it locally. Blat is free for non-profit, academic or personal
use but a license is required for commercial use. The instructions on
downloading Blat are here:
http://genome.ucsc.edu/FAQ/FAQblat#blat3

Alternatively, I have a Perl script that submits 25 sequences at a time
to the web-based Blat, with a pause between submissions so obeying our
rules for using Blat. If you let me know if you would like to obtain that,
I can send you the script.

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 Fri, 10 Nov 2006, Wes Barris wrote:

> Hi,
>
> I am using your web site to blat about 800 ESTs against the mouse genome.
> I have to break this file into smaller files of 25 sequences each to do
> this.  Is there a better way?
>
> The reason I am asking is because I just got this message from your web site:
>
>
> There is a very high volume of traffic coming from your site (IP address 140.253.146.35) as of Thu Nov 9 19:40:17 2006 (California time). So that other users get a fair share of our bandwidth we are
> putting in a delay of 10.0 seconds before we service your request. This delay will slowly decrease over a half hour as activity returns to normal. This high volume of traffic is likely to be due to
> program-driven rather than interactive access, or due to submitting queries on a large number of sequences. If you are making large batch queries please write genome at cse.ucsc.edu and inquire to see if
> there are more efficient ways to access our data. If you are sharing an IP address with someone else's large batches we apologize for the inconvenience. Please contact genome-www at cse.ucsc.edu if you
> think this delay is being imposed unfairly.
> --
> Wes Barris <wes.barris at csiro.au>
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