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

Jason Stajich jason at cgt.duhs.duke.edu
Sun Jan 18 13:07:23 EST 2004

spliced_seq is the answer -
 this is covered a number of times in the archives -
http://search.open-bio.org and in the FAQ

On Sun, 18 Jan 2004, [iso-8859-1] Valentin Ruano wrote:

> 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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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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