[Bioperl-l] populating gbrowse with genomic data rapidly

[rajesh gollapudi]

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

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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