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

[Leighton Pritchard]

Sorry - clicked 'send' while moving windows round when composing... Full
email coming soon...

Apologies,

L.

On 09/04/2010 Friday, April 9, 14:29, "Chris Fields" <cjfields at illinois.edu>
wrote:

> 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
> 
> 
> 
> 
> 
> ______________________________________________________________________
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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


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