[Bioperl-l] bp_genbank2gff3.pl - circular genomes, origin-spanning features, and GFF3
lpritc at scri.ac.uk
Fri Apr 9 09:30:25 EDT 2010
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On 09/04/2010 Friday, April 9, 14:29, "Chris Fields" <cjfields at illinois.edu>
> Didn't see the GFF3 in question.
> On Apr 9, 2010, at 8:06 AM, Leighton Pritchard wrote:
>> (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
>> sequence origin:
>> gene join(92527..92721,1..2502)
>> CDS join(92527..92721,1..2502)
>> /product="ToxR-regulated lipoprotein"
>> 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
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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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