[Biopython-dev] Fwd: [Gmod-schema] GFF3 Is_circular

[Peter]

Hi Brad,

Something to be aware of for GFF work - the spec finally has explicit
support for circular genomes :)

Peter

---------- Forwarded message ----------
From: Andrew McArthur <amcarthur at mac.com>
Date: Wed, Jul 14, 2010 at 5:17 PM
Subject: [Gmod-schema] GFF3 Is_circular
To: gmod-schema at lists.sourceforge.net


Hello all,
The definition of GFF3 at the Sequence Ontology site
(http://www.sequenceontology.org/gff3.shtml) now has format
definitions for supporting circular molecules such as plasmids or
bacterial genomes.  This is done using a new Is_circular flag in the
GFF3 attributes field.  Notably, "For features that cross the origin
of a circular feature (e.g. most bacterial genomes, plasmids, and some
viral genomes), the requirement for start to be less than or equal to
end is satisfied by making end = the position of the end + the length
of the landmark feature."
Are Chado 1.1 and gmod_bulk_load_gff3.pl supporting this change to
GFF3 or should I wait before changing my GFF3 files?
Thanks,
Andrew McArthur

------
Andrew G. McArthur, Ph.D.
Bioinformatics Consulting Services
Email: amcarthur at mac.com, Web: http://mcarthurlab.blogspot.com
Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
AIM: amcarthur at mac.com, Skype: agmcarthur



------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-schema mailing list
Gmod-schema at lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/gmod-schema