[Bioperl-l] gbf to gff

Scott Cain scott at scottcain.net
Wed Jun 3 14:11:54 EDT 2009

Hi Shalabh,

Do you want them combined onto a single reference sequence?  I'm
guessing this is a circular microbial genome in two segments.  Do you
know how to the coordinates in one genbank file relates to the other
(or are you willing to make something up)?  I imagine the way I would
do it would be to convert both files to gff and then write a quicky
script to convert the coordinates and reference sequence name (column
1) of one file to be consistent with the other.


On Wed, Jun 3, 2009 at 1:27 PM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hi all,                 I am working on Roseobacters. Many times I've
> converted gbk file from GenBank to gff format but now one genome
> "Silicibacter lacuscaerulensis" does not have a gbk file instead it has two
> gbf files:
> https://research.venterinstitute.org/moore/SingleOrganism.do?speciesTag=SL1157&pageAttr=pageMain
> So now how i can convert this genome to one gff file so i can use it in
> gbrowse?
> I would really appreciate if anyone can help me out.
> Thanks
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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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