[Bioperl-l] bp_genbank2gff3.pl - circular genomes, origin-spanning features, and GFF3
lpritc at scri.ac.uk
Fri Apr 9 09:06:33 EDT 2010
(cc'd to Lincoln due to GFF3 relevance)
I've recently been trying to use BioPerl, CHADO and GBROWSE to represent
bacterial genome sequences. In doing this, I've been testing with GenBank
genome/feature files, converting these to GFF3 with bp_genbank2gff3.pl to
get a CHADO-friendly gene model. There appears to be an issue when
converting GenBank files that contain features which span the genomic
For example, the GenBank file NC_002127.gbk describes a plasmid from E.coli
O157H7. This contains the following feature which spans the reference
When using the bp_genbank2gff3.pl script (either from bioperl-live or
release 1.6.1) to convert NC_002128.gbk to GFF3 with the command-line
$ bp_genbank2gff3.pl ./Escherichia_coli_O157H7/NC_002128.gbk -out stdout >
This produces the following, non-sequence ontology-compatible GFF:
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C tel:+44(0)1382 562731 x2405
SCRI, Invergowrie, Dundee, DD2 5DA.
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