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

[Chris Fields]

Leighton,

Didn't see the GFF3 in question.

chris

On Apr 9, 2010, at 8:06 AM, Leighton Pritchard wrote:

> 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