[Bioperl-l] bp_genbank2gff3.pl

Scott Cain scott at scottcain.net
Sat Sep 18 05:17:24 EDT 2010

Hi Dave,

bp_genbank2gff3.pl suffers from the fact that it has to deal with
GenBank files :-)  It was designed initially to work on whole genome
refseqs, and contains several ad hoc rules for trying to make it "do
the right thing."  In practice, it is not unusual for a post
processing step (either by hand or a quicky perl script) to be
required to really get it right.  I don't recall the specifics (if I
ever knew :-) for when and how the locus tag is used, but I do know
that there is a list of things that it will try to use for the ID, and
while the locus is on the list, I don't know where it comes in the
list, so it's possible that other items might supersede it.


On Sat, Sep 18, 2010 at 10:05 AM, David Breimann
<david.breimann at gmail.com> wrote:
> Hello,
> I'm not sure how bp_genbank2gff3.pl works. Sometimes it adds a `locus_tag`
> in the fields and sometime it doesn't, even though the genabank has a locus
> tag.
> Also, is the ID always equivalent to the locus tag?
> Thanks,
> Dave
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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

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