[Bioperl-l] How to obtain the nucleotide coding sequence.

Brian Osborne brian_osborne at cognia.com
Sun Jan 18 13:19:26 EST 2004


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Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Valentin Ruano
Sent: Sunday, January 18, 2004 11:44 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] How to obtain the nucleotide coding sequence.

Hi all,

Given a full nucleotide sequence in EMBL format. I
would like to obtain the CDS corresponding
subsequence, that is, free of any non-coding trailing,
-leading or intron segments.

I see how it may be done using the splicing
information encoded in the (join(...)) CDS feature
value. However I'm wondering whether there is some
package that does it already; I do not what to
reinvent the wheel.

Any clues, where I can find shuch functionality?

 thanks in advance, Valentin.

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