[Bioperl-l] bp_genbank2gff3.pl

David Breimann david.breimann at gmail.com
Sat Sep 18 05:20:33 EDT 2010


Since locus_tag is an essential tag in genbank, I suggest locus_tag will be
always added to the GFF last column if it exists in the genbank, whether it
is used as ID in the GFF or not.

On Sat, Sep 18, 2010 at 11:17 AM, Scott Cain <scott at scottcain.net> wrote:

> 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.
>
> Scott
>
>
> 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
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> ------------------------------------------------------------------------
> 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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