[Bioperl-l] populating gbrowse with genomic data rapidly

[rajesh gollapudi]

Hello Dan,
As per this url (http://gmod.org/wiki/Migrating_from_GBrowse_1.X_to_2.X),
there isn't much different between gbrowse1.X and 2.X conf files. Personally
I haven't tried it, but I am confident that it will work.

Rajesh


On Fri, May 15, 2009 at 8:53 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> 2009/5/15 rajesh gollapudi <rajgolla at indiana.edu>:
> > Hello Liam,
> > We have developed a tool called WebGBrowse which could be the solution to
> > your problem. You can find it at http://webgbrowse.cgb.indiana.edu.
> >
> > WebGBrowse serves as a configuration utility for GBrowse, so that users
> can
> > visualize their genomes in gff3 format. It creates a configuration file
> for
> > you, based on the tracks available. In the end you could even download
> the
> > configuration file and use it on your installation of GBrowse.
> > Alternatively, you can use the version of GBrowse provided by this tool
> too.
> > You can find a tutorial on how to use WebGBrowse at
> > http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html
>
> I really like this service, but can you confirm that it will create
> configuration files compatible with GBrowse 2.0?
>
> Dan.
>
>
> > Rajesh
> >
> >
> > On Thu, May 14, 2009 at 11:01 PM, Lincoln Stein <lincoln.stein at gmail.com
> >wrote:
> >
> >> Hi Liam,
> >>
> >> You'll find a bunch of genomes in gff3 format here:
> >>
> >> http://www.gbrowse.org/wiki/index.php/Main_Page
> >>
> >> I think you can simply load them up into gbrowse databases.
> >>
> >> Unfortunately you won't be able to find ready-to-go configuration files
> for
> >> gbrowse2. If they have gbrowse configuration files at all, they will be
> for
> >> gbrowse version 1, which is similar, but not identical. So I'm afraid
> >> you'll
> >> have to inspect the gff3 files and figure out what tracks you want to
> show,
> >> and then write the track config sections.
> >>
> >> If you like, I can send you some ready-made gbrowse2 config/gff3 sets
> for
> >> worm and fly genes. Add this to the yeast example, and you'll have three
> >> genomes to show.
> >>
> >> Lincoln
> >>
> >> On Thu, May 14, 2009 at 10:48 PM, Liam Elbourne <
> lelbourn at cbms.mq.edu.au
> >> >wrote:
> >>
> >> > Hi Lincoln (and all),
> >> >
> >> > This is really a gbrowse specific, and not a particularly bioperly
> >> > question, but I'm not on a gbrowse list, and I figured other bioperl
> >> people
> >> > were likeliest to know how to help.
> >> >
> >> > I've (to all appearances) completely successfully installed
> gbrowse(2.0),
> >> > with some minor glitches mainly caused by typos in the instructions,
> >> which I
> >> > will pass on in due course. The demo data looks great.
> >> >
> >> >  I've been asked (spelt begged, ordered, requested, commanded) if at
> all
> >> > possible to get about 6/7 genomes available for browsing by Sunday
> (USA
> >> > time) for a meeting. I've skimmed the tutorial (which looks excellent,
> >> thank
> >> > you Lincoln!) and started working through it, but wondered if
> somewhere
> >> > there was a cheat sheet or "Dummies guide to stuffing gbrowse full of
> >> Genome
> >> > Data" that would allow me to get these genomes up by then. I know
> there
> >> is a
> >> > script for converting genbank data to gff, which will get me part of
> the
> >> way
> >> > there, as most or all of the genomes have annotation in genbank
> format,
> >> so
> >> > from my attempts to date (yesterday afternoon) I would say that what I
> >> need
> >> > is:
> >> >
> >> >  * appropriately setup .conf files
> >> >  * and instructions on how the data needs to formatted (ie what has to
> go
> >> > into the gff files)  named and located (presumably all in the
> "databases"
> >> > directory), in order to 'match' the .conf files.
> >> >
> >> > Absolutely any assistance would be appreciated, including "it's
> >> completely
> >> > impossible, give up now!" or I guess potentially "it's all in the
> >> > instructions", which I'm sure it is...  I apologise in advance if
> there
> >> is
> >> > already a short guide available on the GMOD wiki or elsewhere that I
> have
> >> > missed, and will happily thank whoever will point me towards it!
> >> >
> >> >
> >> > Regards,
> >> > Liam.
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > ______________________________
> >> >
> >> > Dr Liam Elbourne
> >> > Research Fellow (Bioinformatics)
> >> > Paulsen Laboratory
> >> > Macquarie University
> >> > Sydney
> >> > Australia.
> >> >
> >> >
> >> >
> >>
> >>
> >> --
> >> Lincoln D. Stein
> >> Director, Informatics and Biocomputing Platform
> >> Ontario Institute for Cancer Research
> >> 101 College St., Suite 800
> >> Toronto, ON, Canada M5G0A3
> >> 416 673-8514
> >> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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> >>
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