[Bioperl-l] [Gmod-schema] bp_genbank2gff3.pl in bioperl-live: why map CDS to gene_component_region?

Tue Mar 23 18:18:46 UTC 2010

Hi Leighton,

I wonder if this is a change stemming from Nathan's work on this
script.  Nathan?

Scott

On Tue, Mar 23, 2010 at 12:35 PM, Leighton Pritchard
<Leighton.Pritchard at scri.ac.uk> wrote:
> Hi,
>
> I can't seem to find any discussion of this on the mailing list archives (if
> anyone has a link, I'll happily follow it), so I was wondering what the
> rationale was for the bp_genbank2gff3.pl script as modified in bioperl-live
> mapping CDS features to gene_component_region.
>
> For example, if I use the script on the E.coli sequence/annotation
> NC_000913.gbk, the gene:
>
>     gene            190..255
>                     /gene="thrL"
>                     /locus_tag="b0001"
>                     /note="synonyms: ECK0001, JW4367"
>                     /db_xref="EcoGene:EG11277"
>                     /db_xref="ECOCYC:EG11277"
>                     /db_xref="GeneID:944742"
>     CDS             190..255
>                     /gene="thrL"
>                     /locus_tag="b0001"
>                     /function="leader; Amino acid biosynthesis: Threonine"
>                     /function="1.5.1.8 metabolism; building block
>                     biosynthesis; amino acids; threonine"
>                     /note="GO_process: threonine biosynthetic process [goid
>                     0009088]"
>                     /codon_start=1
>                     /transl_table=11
>                     /product="thr operon leader peptide"
>                     /protein_id="NP_414542.1"
>                     /db_xref="ASAP:ABE-0000006"
>                     /db_xref="UniProtKB/Swiss-Prot:P0AD86"
>                     /db_xref="GI:16127995"
>                     /db_xref="EcoGene:EG11277"
>                     /db_xref="ECOCYC:EG11277"
>                     /db_xref="GeneID:944742"
>                     /translation="MKRISTTITTTITITTGNGAG"
>
> Is mapped to
>
> NC_000913       GenBank region  190     255     .       +       .
> ID=GenBank:region:NC_000913:190:255
> NC_000913       GenBank exon    190     255     .       +       .
> ID=GenBank:exon:NC_000913:190:255
> NC_000913       GenBank gene    190     255     .       +       .
> ID=b0001;Dbxref=EcoGene:EG11277,ECOCYC:EG11277,GeneID:944742;Note=synonyms:
> ECK0001%2C JW4367;gene=thrL;locus_tag=b0001
> NC_000913       GenBank gene_component_region   190     255     .       +
> .
> Parent=b0001;Dbxref=ASAP:ABE-0000006,UniProtKB/Swiss-Prot:P0AD86,GI:16127995
> ,EcoGene:EG11277,ECOCYC:EG11277,GeneID:944742;Note=GO_process: threonine
> biosynthetic process [goid
> 0009088];Ontology_term=GO:0009088;codon_start=1;function=leader%3B Amino
> acid biosynthesis: Threonine,1.5.1.8 metabolism%3B building block
> biosynthesis%3B amino acids%3B
> threonine;gene=thrL;locus_tag=b0001;product=thr operon leader
> peptide;protein_id=NP_414542.1;transl_table=11;translation=MKRISTTITTTITITTG
> NGAG
>
> I understand the region-exon-gene part of the model, but not the
> gene_component_region, which appears to be a catch-all.  I would have
> assumed that the CDS is better mapped to a polypeptide, as described in the
> CHADO documentation:
>
> http://gmod.org/wiki/Chado_Best_Practices#Canonical_Gene_Model
>
> There is no difference in script output whether --CDS or --noCDS is used.
>
> Cheers,
>
> L.
>
> --
> 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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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research