From GFF2 to GFF3

tianping · 04-18-2011, 02:34 AM

Dear all,

We are sequencing an animal genome and the produced GFF file is version 2. However, I learned that GFF2 is now deprecated and GFF3 is a better choice. So I want a GFF3 file for the genome. Since I am not in charge of GFF production, I want to ask some questions here before submitting my request to the research group.

My questions are (1)How is GFF3 file produced? Is it difficult to turn from GFF2 to GFF3? Does it take much effort? (2) What softwares are available that support GFF3? GMOD mentions that Apollo, Chado, CMap and GBrowse support GFF3. Softwares based on Chado such as Artemis and ACT also support. Any more?

Many thanks!

PS: I have changed the question title to avoid misunderstanding. My purpose is to learn how to get a GFF3 file. I want to annotate the genome using GFF3.

Simon Anders · 04-18-2011, 03:00 AM

When going from GFF2 to GFF3, be sure to read this thread on the Bioconductor mailing list where we found that everything is even more messed up than it seems.

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04-18-2011, 02:34 AM	#1
tianping Junior Member Location: Shenzhen Join Date: Apr 2011 Posts: 2	How to get GFF3 files? Dear all, We are sequencing an animal genome and the produced GFF file is version 2. However, I learned that GFF2 is now deprecated and GFF3 is a better choice. So I want a GFF3 file for the genome. Since I am not in charge of GFF production, I want to ask some questions here before submitting my request to the research group. My questions are (1)How is GFF3 file produced? Is it difficult to turn from GFF2 to GFF3? Does it take much effort? (2) What softwares are available that support GFF3? GMOD mentions that Apollo, Chado, CMap and GBrowse support GFF3. Softwares based on Chado such as Artemis and ACT also support. Any more? Many thanks! PS: I have changed the question title to avoid misunderstanding. My purpose is to learn how to get a GFF3 file. I want to annotate the genome using GFF3. Last edited by tianping; 04-18-2011 at 03:10 AM. Reason: misleading title

04-18-2011, 03:00 AM	#2
Simon Anders Senior Member Location: Heidelberg, Germany Join Date: Feb 2010 Posts: 994	When going from GFF2 to GFF3, be sure to read this thread on the Bioconductor mailing list where we found that everything is even more messed up than it seems.