[Gmod-gbrowse] GBrowse 2.07 on CPAN

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[Gmod-gbrowse] GBrowse 2.07 on CPAN

Lincoln Stein
Hi all,

I just released the following packages to CPAN:
  • GBrowse 2.07 -- fixes problems relating to SAM file downloads when running under mod_perl and fastCGI. Also fixes a long-standing bug in which the user searches for a nonexistent feature, hits the back button, and tracks fail to redisplay.
  • Bio::Graphics 2.09 -- fixes a problem in which a subroutine was defined in init_code but not recognized when later referenced by a callback.
  • Bio-SamTools 1.19 -- Fixed bugs relating to cigar string display (string was garbled); added a method to get the seq_id of the mapped mate, and another method to print out SAM lines from the Alignment object.
I apologize for the series of releases over the last week, but the new performance-enhancing configuration caching code in Bio::Graphics broke a number of obscure features. I think this is a pretty good release (but I said that last time!)

Best,

Lincoln

--
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 <[hidden email]>

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Re: [Gmod-gbrowse] GBrowse 2.07 on CPAN

Keiran Raine
Hi Lincoln,

There is a bug in the protein translation overlay of the gene glyph.  
I've checked and this is not due to 2.08->2.09 Bio-Graphics changes.

In human 37 (hg19), 1:6692428..6692477

As you can see in the attached image the third transcript is showing a  
translation that does not appear to be possible.  The second zoomed  
out image shows what appears to be happening.

Let me know if I can provide any further information.

Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100
[hidden email]




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 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.







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Re: [Gmod-gbrowse] GBrowse 2.07 on CPAN

Lincoln Stein
Ouch.

Lincoln

On Tue, May 18, 2010 at 5:45 AM, Keiran Raine <[hidden email]> wrote:
Hi Lincoln,

There is a bug in the protein translation overlay of the gene glyph.  I've checked and this is not due to 2.08->2.09 Bio-Graphics changes.

In human 37 (hg19), 1:6692428..6692477

As you can see in the attached image the third transcript is showing a translation that does not appear to be possible.  The second zoomed out image shows what appears to be happening.

Let me know if I can provide any further information.

Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100
[hidden email]




--
The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice is 215 Euston Road, London, NW1 2BE.










--
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 <[hidden email]>

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