[Bioperl-l] Re: [Gmod-gbrowse] Translation glyph
Aaron J. Mackey
amackey at pcbi.upenn.edu
Thu Sep 22 21:11:33 EDT 2005
Somehow, even though I sing the alphabet song to my son nearly every
day, I couldn't remember V. It's been fixed.
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
> 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.
>> is depending on Bio::Tools::CodonTable. The translate() method of the
>> latter only returns single amino acid codes. However,
>> *is* aware of threeletter codes but only in the context of
>> One could change the behaviour of B::T::CodonTable, though. But I
>> know whether the resulting Bio::PrimarySeq will be valid for bioperl.
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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)
postal: Penn Genomics Institute
Goddard Labs 212
415 S. University Avenue
Philadelphia, PA 19104-6017
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