[EMBOSS] extracting 3' UTRs

[David.Bauer at SCHERING.DE]

Hi Shrish,

in principle this would be an easy task for 'extractfeat' because the EMBL
feature table definition contains also the feature key "3' UTR".
But nearly nobody uses this feature key in praxi.
So I would use coderet to look for the end of a CDS and then extract the
remaining part with seqret. or extractseq.
It will be straightforward for single mRNA entries with one CDS.
If you want to do this on a genome level, you should take a look at
Ensembl (www.ensembl.org) and the Mart interface. There you can extract
3'UTR.
But from my experience the annotation of UTRs is very incomplete so don't
expect to get something comprehensive with these methods.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 16/01/2007 15:49:53:

> Hi Shrish
>
> So far as I know, not directly, but it's easily done using a combination
> of e.g. coderet, getorf, plotorf and seqret.
>
> Should be obvious from the documentation, e.g.
> http://emboss.sourceforge.net/apps/cvs/index.html
> http://emboss.sourceforge.net/docs/emboss_tutorial/node4.html
>
> If you envisage a single tool for your task, please let us know to
> emboss-bug at emboss.open-bio.org please)
>
> Cheers
>
> Jon
>
>
>
>
> > Hi!
> > Is there a way to extract 3' UTRs using EMBOSS programs?
> > Shrish
> > Dr. Shrish Tiwari
> > E503, Centre for Cellular and Molecular Biology
> > Uppal Road, Hyderabad - 500 007, INDIA
> > Phone: 91-40-27192777
> > Alternate email: shrish.geo at yahoo.com
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss
> >
>
>
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