[Bioperl-l] BLINK PARSER

[Mark A. Jensen]

Hi Sanjay-
I'm not sure BioPerl has an interface specifically for BLINK (I will
be corrected if I'm wrong, so stay tuned). If you can obtain the
"raw" blast output for the protein you're interested in ( doing
[BLINK] then [Other Views: BLAST] then [Format:Show: Alignment as Plain text] )
that text can be parsed using the Bio::SearchIO tools, and you can use 
Bio::Search::Tiling
to obtain the 'best' hsps. This may not be too helpful, I'm afraid, but it is 
where
I would start.
Mark
----- Original Message ----- 
From: "sanjay singh" <sanjaysingh765 at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Saturday, August 15, 2009 9:38 AM
Subject: [Bioperl-l] BLINK PARSER


> Hi,
> I want to submit query to NCBI'S BLINK and parsed the result for the best
> hit. is there anyone have script to do so.i would be very grateful if
> someone would like to share it with me.
> regards
> sanjay
>
> -- 
> Happy moments ,  praise God.
> Difficult moments,  seek God.
> Quiet moments,  worship God.
> Painful moments,  trust God.
> Every moment,  thank God
>
> Sanjay Kumar Singh
> Bose Institute
> 93\1,A.P.C.Road
> Kolkata-700 009
> West Bengal
> India
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