[BioRuby] selenoproteins

[Toshiaki Katayama]

Hello,

On 2004/06/19, at 1:07, GOTO Naohisa wrote:
> On Tue, 15 Jun 2004 18:11:48 +0200
> Michael Han <m.han at gsf.de> wrote:
>
>> Hi everyone,
>>
>> i am working on fine-tuning an annotation pipeline with ruby.
>> As selenoproteins seem not to be supported by BioRuby, they break my
>> assertions (and most gene predictions).
>> Therefore i would like to add a codon-table for selenoproteins  
>> (TGA=>U).
>
> In next version, Bio::Sequence::NA#translate and Bio::CodonTable will  
> be
> changed, and users will be able to modify codon tables freely based on
> NCBI taxonomy's definitions or from scratch. We'll soon commit new  
> codes
> into CVS in few days.

I have committed these changes into CVS.

* Bio::CodonTable is now changed to be a class.
* Bio::Sequence::NA#translate method accepts Bio::CodonTable object.

You can use your own table and its definition as follows:

   hash = { 'atg' => 'M', ... }
   definition = "my table"
   ct = Bio::CodonTable.new(hash, definition)

Selecting from hard coded tables is same as before:

   ct = Bio::CodonTable[1]

We have also implemented 'revtrans', 'start_codon?' and 'stop_codon?'
methods.  Please take a look at test codes and documents added at the
bottom of codontable.rb file.

http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby/lib/bio/ 
data/codontable.rb?rev=0.10&cvsroot=bioruby&content-type=text/ 
vnd.viewcvs-markup

Additionally, Bio::Sequence::NA#translate method is made 30-50% faster
than before with the code contributed by N. Goto.

Regards,
Toshiaki Katayama
--
Human Genome Center, Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
tel://+81-3-5449-5614, fax://+81-3-5449-5434
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