Kevin Brown | 2 Aug 00:43 2006

Re: Getting sequences by base pair locations

Perl Mechanize is a great way to submit web forms repeatedly.  I do it
for things like MHC epitope prediction sites as well as a way to grab
things like journal articles matching certain keywords. 

> -----Original Message-----
> From: bioperl-l-bounces <at> 
> [mailto:bioperl-l-bounces <at>] On Behalf Of 
> Cook, Malcolm
> Sent: Tuesday, August 01, 2006 8:12 AM
> To: Yuval Itan; bioperl-l <at>
> Subject: Re: [Bioperl-l] Getting sequences by base pair locations
> Yuval,
> Glad to help.  Given that you are not running blat suite 
> locally, but at
> ucsc, you should try this approach:
> upload/paste your blat results (in blat's native output 
> format, psl) as
> a custom track in the genome browser, named, say, myhumanhits
> (i.e. just give the blat results a new first line like: `track
> name="myhumanhits" description="myhumanhits from my favorite human
> genes" visibility=2`)
> then goto the table browser and configure it 
> 	group = 'custom tracks'
> 	track = 'myhumanhits'
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