[Bioperl-l] populating gbrowse with genomic data rapidly

Lincoln Stein lincoln.stein at gmail.com
Thu May 14 23:01:07 EDT 2009

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 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.


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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