[BioRuby] selenoproteins

[Michael Han]

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).

Also i would like to ask if there are people working on support for 
BLAT / BED / PSL / moving tests into separate Test::Unit classes.

greetings,

Michael Han
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Institute for Bioinformatics
National Research Center for Environment and Health
Munich - Germany
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i am thinking of something like adding to bio/data/codontable.rb
------------------------  8< ---------------
# codon table 99  - selenoproteins (Eukaryote)
     99 => {
       'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
       'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
       'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'U',
       'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',

       'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
       'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
       'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
       'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',

       'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
       'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
       'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
       'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',

       'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
       'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
       'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
       'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
     },
----------------------- 8< -------------------------