[Bioperl-l] GFF to GTF

Cook, Malcolm MEC at stowers-institute.org
Wed Nov 9 10:48:10 EST 2005

GFF as a format has a variety of versions.  AFAIK, GTF is GFF 2.1 or 2.5

The main differences have to do with format and semantics of GFF's
column 9, the inclusion of sequence data itself in the file, and 

version   reference
1 &  2    http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
2.1       http://genes.cs.wustl.edu/GTF21.html
2.5       ref?
3         http://song.sourceforge.net/gff3.shtml

What is your source of GFF? It is possible that your GFF annotation
already is GTF.  What version is it?  Look in the file.  There may be a
'##gff-version' directive in it.  Or, if you see that column 9 looks
like 'gene_id "381.000"; transcript_id "381.000.1";' (c.f. gff 2.1 docs)
then it probably already is in GTF.

If it is NOT already GTF (GFF 2.1 or 2.5), then you must provide example
expected input and output to see if we (I) can help further. 


Malcolm Cook - mec at stowers-institute.org - 816-926-4449
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, MO  USA 

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Filipe
Sent: Tuesday, November 08, 2005 8:18 AM
To: Bioperl
Subject: [Bioperl-l] GFF to GTF

Hi all,

I'm currently trying to use a software called Projector to predict 
genes. As input it needs two sequences and the anotation of one of them 
in GTF. As the info in GTF is included in the GFF I was thinking of 
getting a way to convert the GFF files into GTF. I thought of using the 
Bioperl module for GFF to parse the GFF and write the GTF fields to an 

Does anyone knows if there's any script already made? Or of a simple way

to do it?

Thanks in advance

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