[Bioperl-l] Bio::Graphics/Bio::DB::GFF sequence browser released

[Lincoln Stein]

Hi All,

I've just released a web browser for sequence annotation data based on
the MODules Bio::Graphics module.  It uses MySQL and the Bio::DB::GFF
module from Bioperl as its underlying database and middleware layer.

Features:

	1) an overview of the whole chromosome (or contig), showing
	   landmarks like genetic markers, or cytogenetic bands.

	2) detailed view with 8 levels of zoom (configurable)

	3) outgoing links to the URL of your choice, can follow global
	   rules or calculate the URL on a feature-by-feature basis

	4) user can select among multiple data sources, adjust the
	   size of the image, and control which features are being
	   shown (but not reorder them, currently)

	5) flexible search options.  You can search for anything
	   that's in the group field, such as a gene name, chromosome
	   name, clone name, primer pair, genetic marker, etc.

	6) user's settings are retained persistently.  When he comes
	   back, he's taken to the last region he was viewing.

	7) highly-customizable using a single configuration file.
	   Adding a new annotation type is as easy as adding a
	   new line to the configuration file.

	8) no dependency on a particular database schema.  Anything
	   that can go into a GFF file can be displayed.

	9) once you install this browser, you also have a DAS
	   (distributed annotation system) server for free.

I wanted to compare it to the standard WormBase browser, whose look
and feel it closely mimics, so the demo version is installed on
wormbase at this URL:

	 http://www.wormbase.org/db/seq/gbrowse

The plan this week is to bring in Chris's FlyBase GFF files, and see
how it performs on that data.  Has anyone written a polytene
chromosome glyph to use for the overview?

Performancewise, the browser feels a lot faster than the standard
wormbase browser, but that might be because not so many people are
hitting it.  In any case, it's worth asking the wormbase-dev group
whether it's worth the administrative hassle to convert wormbase over
to using this.  It would involve having to maintain a MySQL database
as well as AceDB, which would make live more complicated for the
mirrors.

Lincoln

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY

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