[Bioperl-l] populating gbrowse with genomic data rapidly
dan.bolser at gmail.com
Fri May 15 08:53:16 EDT 2009
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
I really like this service, but can you confirm that it will create
configuration files compatible with GBrowse 2.0?
> 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:
>> 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
>> 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.
>> On Thu, May 14, 2009 at 10:48 PM, Liam Elbourne <lelbourn at cbms.mq.edu.au
>> > 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
>> > 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,
>> > you Lincoln!) and started working through it, but wondered if somewhere
>> > there was a cheat sheet or "Dummies guide to stuffing gbrowse full of
>> > 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
>> > there, as most or all of the genomes have annotation in genbank format,
>> > from my attempts to date (yesterday afternoon) I would say that what I
>> > 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
>> > 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
>> > 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>
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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