[Bioperl-l] bp_genbank2gff3.pl in bioperl-live: why map CDS to gene_component_region?
Leighton.Pritchard at scri.ac.uk
Tue Mar 23 12:35:42 EDT 2010
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:
/note="synonyms: ECK0001, JW4367"
/function="leader; Amino acid biosynthesis: Threonine"
/function="18.104.22.168 metabolism; building block
biosynthesis; amino acids; threonine"
/note="GO_process: threonine biosynthetic process [goid
/product="thr operon leader peptide"
Is mapped to
NC_000913 GenBank region 190 255 . + .
NC_000913 GenBank exon 190 255 . + .
NC_000913 GenBank gene 190 255 . + .
NC_000913 GenBank gene_component_region 190 255 . +
biosynthetic process [goid
acid biosynthesis: Threonine,22.214.171.124 metabolism%3B building block
biosynthesis%3B amino acids%3B
threonine;gene=thrL;locus_tag=b0001;product=thr operon leader
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
There is no difference in script output whether --CDS or --noCDS is used.
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
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SCRI, Invergowrie, Dundee, DD2 5DA.
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