[Bioperl-l] bp_genbank2gff3.pl - circular genomes, origin-spanning features, and GFF3

[Leighton Pritchard]

Hi,

(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
origin.

For example, the GenBank file NC_002127.gbk describes a plasmid from E.coli
O157H7.  This contains the following feature which spans the reference
sequence origin:

     gene            join(92527..92721,1..2502)
                     /gene="tagA"
                     /locus_tag="pO157p01"
                     /db_xref="GeneID:1789672"
     CDS             join(92527..92721,1..2502)
                     /gene="tagA"
                     /locus_tag="pO157p01"
                     /codon_start=1
                     /transl_table=11
                     /product="ToxR-regulated lipoprotein"
                     /protein_id="NP_052607.1"
                     /db_xref="GI:10955349"
                     /db_xref="GeneID:1789672"

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 >
test.gff3

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


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