[Genome] blat queries (fwd)

[Rachel Harte]

I, of course, meant "Blat Perl scripts" below, not "Blast Perl scripts".

Rachel

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


---------- Forwarded message ----------
Date: Mon, 30 Apr 2007 10:55:46 -0700 (PDT)
From: Rachel Harte <hartera at soe.ucsc.edu>
To: Sung Kim <sungkkim at usc.edu>
Cc: genome at cse.ucsc.edu
Subject: Re: [Genome] blat queries

Hello Sung Kim,

There are two ways that you can easily do this:

1) Download the Blat executable and run Blat locally. See:
http://genome.ucsc.edu/FAQ/FAQblat#blat3
It is free for academic, non-profit and personal use.

Genome sequences can be obtained from the downloads server:
http://hgdownload.cse.ucsc.edu/downloads.html

If you click on a link to an organism of interest and then click on the
"Full data set" or "Data set by chromosome", you can get the genome
sequences.

You can also get sequence files by chromosome in nib format or a whole
genome in 2bit format both of which may be used as input to Blat. These
can be obtained from the downloads server by ftp:
ftp://hgdownload.cse.ucsc.edu/gbdb/<database>/<database>.2bit
ftp://hgdownload.cse.ucsc.edu/gbdb/<database>/nib/*.nib

where database is the assembly name e.g. hg18, mm8 etc.

2) You can use these Blast Perl scripts:
http://genomewiki.ucsc.edu/index.php/Blat_Scripts

BlatBot.pl will access our Blat server directly. If you use this script,
please observe our usage guidelines:

http://genome.ucsc.edu/FAQ/FAQblat#blat2

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 Sun, 29 Apr 2007, Sung Kim wrote:

> Hi,
> I would like to make large queries onto blat and was wondering how i can do this efficiently. i have about ~1000 sequences <300bp that i would like to blat against the most recent build of the human genome.
>
>
> thank you
>
> sung kim
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
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