[Bioperl-l] extract UTR from cds and mRNA coordinates

Jason Stajich jason at bioperl.org
Thu Sep 9 01:51:53 EDT 2010


Hi Alper -

This script operates on gtf so doesn't quite do what you want but could 
be modified to be simpler to just look at the CDS and mRNA rather than 
the exon,start/stop codon info
   
http://github.com/hyphaltip/genome-scripts/blob/master/data_format/gtf2gff3_3level.pl

Otherwise I think there make be some easy ways to do this from some 
tools in MAKER too.

-jason
Alper Yilmaz wrote, On 9/8/10 9:47 AM:
> Hi,
>
> I have a GFF file listing mRNA and CDS coordinates for every
> transcript of each gene. I need to extract 5'UTR and 3'UTR coordinates
> based on that information. I was wondering, if there's already made
> script for that purpose that you're aware of.
>
> I already uploaded the GFF file into Bio::DB::SeqFeature database, so
> I can utilize both flat file or database based scripts.
>
> thanks,
>
> Alper Yilmaz
> Post-doctoral Researcher
> Plant Biotechnology Center
> The Ohio State University
> 1060 Carmack Rd
> Columbus, OH 43210
> (614)688-4954
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