[Bioperl-l] gbf to gff
Scott Cain
scott at scottcain.net
Wed Jun 3 18:11:54 UTC 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.
Scott
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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