[Bioperl-l] perl ribosome

[Ewan Birney]

On Fri, 22 Nov 2002, [iso-8859-1] Mauricio Herrera Cuadra wrote:

> Hi there!
>
> I'm new to bioperl and I was wondering if there is a ribosome script or
> module which i could use for translating sequences and getting product's
> information. There is one Javascript Ribosome:

In Bioperl 1.2 (due out december) going


use Bio::Perl;

#this wont work until Bioperl 1.2 comes out
$protein_seq = translate_as_string('ATGTTTGGG');

will give you

'MFG' in $protein_seq;



In Bioperl 1.0.2 - which is available now from www.cpan.org, it is little
more complex, you need to go either:

use Bio::Perl(new_sequence);

$seq = new_sequence('ATGTTTGGG','myid');
$trans = $seq->translate();
print "Translation is ",$trans->seq,"\n";


OR


use Bio::Tools::CodonTable;


$codontable = Bio::Tools::CodonTable->new();

$translated_string = $codontable->translate('ATGTTTGGG');

print "Translated is ",$translated_string,"\n";

You can use different genetic codes bu going

# use Echinoderm Mitochondrial
$codontable = Bio::Tools::CodonTable(-id => 9);

   @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
         );




Bio::Tools::CodonTable is the place in Bioperl where the translation
happens - it is worth a read if you are interested. Also check out
web sites at:



EBI Translation Table Viewer:
     http://www.ebi.ac.uk/cgi-bin/mutations/trtables.cgi

NCBI Genetic Codes home page:
     http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c




>
> http://mbt.biobitfield.com/vr.html
>
> which is good, but i would like a perl one where i could add more
> features, any ideas?
>
> Thanks in advance.
> Mauricio.
>
> =====
> MAURICIO HERRERA CUADRA
> arareko@yahoo.com
> http://www.geocities.com/arareko/
>
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