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

[Aaron J. Mackey]

Somehow, even though I sing the alphabet song to my son nearly every  
day, I couldn't remember V.  It's been fixed.

Thanks,

-Aaron

On Sep 22, 2005, at 9:04 PM, Smithies, Russell wrote:

> Looks really good but seems to have a problem with Valine?
>
> -----Original Message-----
> From: Aaron J. Mackey [mailto:amackey at pcbi.upenn.edu]
> Sent: Friday, 23 September 2005 12:56 a.m.
> To: Marc Logghe
> Cc: Smithies, Russell; gmod-gbrowse at lists.sourceforge.net;
> bioperl-l at portal.open-bio.org
> Subject: Re: [Gmod-gbrowse] Translation glyph
>
>
> But the translation glyph code could easily do the necessary
> substitutions.  I agree it should not be done from
> Bio::Tools::CodonTable
>
> 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.
>
> -Aaron
>
> 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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--
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