[Bioperl-l] Extract sequences of CDS regions from Genbank formatted file

[Andreas Leimbach]

Hi Cacau,

there are plenty. The EMBOSS package e.g. has one:
http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/extractfeat.html

There's FeatureExtract from the CBS:
http://www.cbs.dtu.dk/services/FeatureExtract/

I also wrote a script that does that with BioPerl:
https://github.com/aleimba/bac-genomics-scripts/tree/master/cds_extractor

For BioPerl, have a look at the Feature-Annotation HowTo:
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

Best,
Andreas


--
Andreas Leimbach
Universität Münster
Institut für Hygiene
Mendelstr. 7
D-48149 Münster
Germany

Tel.: +49 (0)551 39 33843
E-Mail: andreas.leimbach at uni-wuerzburg.de

On 12.08.2014 21:10, Cacau Centurion wrote:
> Hi all,
>
> I was wondering if there is a way to directly extract all sequences of CDS
> regions from a Genbank formatted file using bioperl?
>
> Yours,
> Cacau
>
>
>
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