[BioRuby] selenoproteins
Toshiaki Katayama
ktym at hgc.jp
Sat Jun 26 11:26:28 EDT 2004
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
BioRuby project http://bioruby.org/~k/
GenomeNet/KEGG http://www.genome.jp/
Human Genome Center http://www.hgc.jp/
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