[Bioperl-l] transcribe...

[Brian Osborne]

Geetha,

There is no such method in Bioperl. Meaning, if you tell Bioperl to
translate, and the sequence in question is DNA, there is no need to create
an intermediate RNA sequence. From the bptutorial:

Many of these methods are self-explanatory. However, bioperl's flexible
translation methods warrant further comment. Translation in bioinformatics
can mean two slightly different things:
1. Translating a nucleotide sequence from start to end.
2. Taking into account the constraints of real coding regions in mRNAs.
The bioperl implementation of sequence-translation does the first of these
tasks easily. Any sequence object which is not of alphabet 'protein' can be
translated by simply calling the method which returns a protein sequence
object:
  $translation1 = $my_seq_object->translate;
However, the translate method can also be passed several optional parameters
to modify its behavior. For example, the first two arguments to
``translate'' can be used to modify the characters used to represent stop
(default '*') and unknown amino acid ('X'). (These are normally best left
untouched.) The third argument determines the frame of the translation. The
default frame is ``0''. To get translations in the other two forward frames,
we would write:
  $translation2 = $my_seq_object->translate(undef,undef,1);
  $translation3 = $my_seq_object->translate(undef,undef,2);
The fourth argument to ``translate'' makes it possible to use alternative
genetic codes. There are currently 16 codon tables defined, including tables
for 'Verterbate Mitochondrial', 'Bacterial', 'Alternative Yeast Nuclear' and
'Ciliate, Dasycladacean and Hexamita Nuclear' translation. These tables are
located in the object Bio::Tools::CodonTable which is used by the translate
method. For example, for mitochondrial translation:
  $human_mitochondrial_translation =
      $my_seq_object->translate(undef,undef,undef, 2);
If we want to translate full coding regions (CDS) the way major nucleotide
databanks EMBL, GenBank and DDBJ do it, the translate method has to perform
more tricks. Specifically, 'translate' needs to confirm that the sequence
has appropriate start and terminator codons at the beginning and the end of
the sequence and that there are no terminator codons present within the
sequence. In addition, if the genetic code being used has an atypical
(non-ATG) start codon, the translate method needs to convert the initial
amino acid to methionine. These checks and conversions are triggered by
setting the fifth argument of the translate method to evaluate to ``true''.
If argument 5 is set to true and the criteria for a proper CDS are not met,
the method, by default, issues a warning. By setting the sixth argument to
evaluate to ``true'', one can instead instruct the program to die if an
improper CDS is found, e.g.
  $protein_object =
      $cds->translate(undef,undef,undef,undef,1,'die_if_errors');
See the Bio::Tools::CodonTable manpage for related details.
Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Vasudevan, Geetha
Sent: Thursday, March 20, 2003 2:50 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] transcribe...


Hello,

What is the method in bioperl to "transcribe" seqs before using
$seq->translate? thanks in advance.

-geetha.

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