Extract sequences of CDS regions from Genbank formatted file

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Extract sequences of CDS regions from Genbank formatted file

Cacau Centurion
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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Re: Extract sequences of CDS regions from Genbank formatted file

Ashton Trey Belew
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  Hello Cacau,
  Attached is a script I use for exactly this purpose.  It also makes
a gff and some other stuff which might be of interest.

  It makes use of Getopt::Long and assumes you will feed it --input or
- -i followed by the genbank file.  If you forget (as I often do), it
will ask you for the genbank filename.
  If you provide -o or --output, that will be the basename of the
following output files:

  1.  A gff of all entries
  2.  A gff of all the gene entries
  3.  A gff of CDS entries
  4.  A gff of the inter-cds regions
  5.  A fasta file of all the coding sequences
  6.  A fasta file of the coding sequences as peptide sequence.

 Good luck,
 -Trey

On 08/12/2014 03:10 PM, 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
>
>
> _______________________________________________ Bioperl-l mailing
> list [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
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=vYIR
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gb2gff.pl (4K) Download Attachment
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Re: Extract sequences of CDS regions from Genbank formatted file

Andreas Leimbach
In reply to this post by Cacau Centurion
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: [hidden email]

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
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
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Re: Extract sequences of CDS regions from Genbank formatted file

Brian Osborne-2
In reply to this post by Cacau Centurion
Cacau,

Oh yes, all of the Bio* languages can do this.

For an introduction to the concepts and some relevant code see:


Brian O.


On Aug 12, 2014, at 3:10 PM, Cacau Centurion <[hidden email]> 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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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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