[Bioperl-l] bioperl translate() function for seq obj

[Mark A. Jensen]

Hi Jarod-

translate() uses NCBI "Standard" table by default. Check out the POD for
PrimarySeqI.pm (where translate is defined). You can specify others by setting
-CODONTABLE_ID => $n as an argument to translate().
The codon tables are in Bio::Tools::CodonTable, where the following are defined:

 @NAMES =   #id
 (
  'Standard',  #1
  'Vertebrate Mitochondrial',#2
  'Yeast Mitochondrial',# 3
  'Mold, Protozoan, and CoelenterateMitochondrial and Mycoplasma/Spiroplasma',#4
  'Invertebrate Mitochondrial',#5
  'Ciliate, Dasycladacean and Hexamita Nuclear',# 6
  '', '',
  'Echinoderm Mitochondrial',#9
  'Euplotid Nuclear',#10
  '"Bacterial"',# 11
  'Alternative Yeast Nuclear',# 12
  'Ascidian Mitochondrial',# 13
  'Flatworm Mitochondrial',# 14
  'Blepharisma Nuclear',# 15
  'Chlorophycean Mitochondrial',# 16
  '', '',  '', '',
  'Trematode Mitochondrial',# 21
  'Scenedesmus obliquus Mitochondrial', #22
  'Thraustochytrium Mitochondrial' #23
  );
Can others (Scott M?) chime in on blast?
Mark

----- Original Message ----- 
From: "云 何" <jarodpardon at yahoo.com.cn>
To: "'bioperl-l'" <Bioperl-l at lists.open-bio.org>
Sent: Thursday, April 09, 2009 8:27 PM
Subject: [Bioperl-l] bioperl translate() function for seq obj


>
>
> Hi, all,
> I want to know whether Bio::PrimarySeqI::translate() uses identical method and 
> codon table with NCBI Blast/blastx does. Thanks.
>
> Jarod
>
>
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