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

[Leighton Pritchard]

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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