[Bioperl-l] New version of gbrowse released

[Lincoln Stein]

Hi all,

The GMOD group has just released a new version of the generic genome browser, 
which can be downloaded from 
http://sourceforge.net/project/showfiles.php?group_id=27707.  Here's the 
highlights from the change log:

	1.45 Sun Jul  7 17:32:08 EDT 2002
	* Major feature release.
	* Added conversion script for human genome annotations from NCBI.
	You can load all the human annotations provided your file system can
	maintain a > 2 Gb file.
	* New CDS/reading frame glyph.
 	* New 6-frame translation glyph.
 	* FASTA dumper now dumps out decorated FASTA files.
 	* Sequence dumper supports output in GenBank, EMBL, GAME, BSML and other
  	formats (thanks to magic of Bio::SeqIO).
 	* Full set of restriction enzymes in restriction enzyme annotator plugin.
 	* Support for named external feature tracks in popup menu.
 	* External feature tracks are now highlighted in selection list.
 	* Fixed uploaded files so that they are persistent.
 	* Minor aesthetic improvements.
 	* REQUIRES: BioPerl 1.02.
 	* STILL PENDING: Internationalization/localization patches

One of the cooler features is Jason Stajich's Sequence Dumper plugin, which 
uses the Bioperl SeqIO system to output the feature tables in a large variety 
of formats including GAME and BSML.  I'm also kind of fond of my own 
reading-frame glyph, which renders graphically the way alternative splicing 
patterns thread among the three reading frames.  This is something that 
biologist Anne Lorraine requested during a digression at the O'Reilly 
bioinformatics meeting, and I think I've finally figured out what it was she 
actually wanted!

The browser requires bioperl 1.02, which isn't released yet.  I've provided a 
patch file to bring bioperl 1.01 up to date, or you can grab the latest and 
greatest via CVS.  Unfortunately I did not have time to get the 
internationalization/localization modules integrated with gbrowse, nor were 
the XY graph (e.g. microarray), PIP, or cytogenetic map modules ready to go.

Lincoln

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