[Bioperl-l] Re: [Gmod-gbrowse] Translation glyph

Aaron J. Mackey amackey at pcbi.upenn.edu
Thu Sep 22 08:55:30 EDT 2005

But the translation glyph code could easily do the necessary  
substitutions.  I agree it should not be done from  

I just checked in the patch to bioperl for translation.pm to enable  
"triletter_code" as an option (defaults to 0).  Give it a try.  I'm  
happy to back it out if there are problems.


On Sep 22, 2005, at 2:36 AM, Marc Logghe wrote:

>> -----Original Message-----
>> From: gmod-gbrowse-admin at lists.sourceforge.net
>> [mailto:gmod-gbrowse-admin at lists.sourceforge.net] On Behalf
>> Of Smithies, Russell
>> Sent: Thursday, September 22, 2005 4:21 AM
>> To: gmod-gbrowse at lists.sourceforge.net
>> Subject: [Gmod-gbrowse] Translation glyph
>> Is it possible to show 3-letter names for 3-frame and 6-frame
>> translation glyphs at high magnification?
>> E.g.  'Phe' instead of 'F'
> I am afraid this is currently not possible AFAIK. B::G::G::translation
> is depending on Bio::Tools::CodonTable. The translate() method of the
> latter only returns single amino acid codes. However, B::T::CodonTable
> *is* aware of threeletter codes but only in the context of
> revtranslate().
> One could change the behaviour of B::T::CodonTable, though. But I  
> don't
> know whether the resulting Bio::PrimarySeq will be valid for bioperl.
> Marc
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Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  amackey at pcbi.upenn.edu
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

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