[Bioperl-l] bioperl translate() function for seq obj
Mark A. Jensen
maj at fortinbras.us
Fri Apr 10 01:16:18 UTC 2009
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
>
>
> ___________________________________________________________
> 好玩贺卡等你发,邮箱贺卡全新上线!
> http://card.mail.cn.yahoo.com/
>
>
--------------------------------------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
More information about the Bioperl-l
mailing list