NAME

Bio::Tools::Run::PiseApplication::transeq

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::transeq

      Bioperl class for:

	TRANSEQ	Translate nucleic acid sequences (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/transeq.html 
         for available values):


		transeq (String)

		init (String)

		sequence (Sequence)
			sequence -- nucleotide [sequences] (-sequence)
			pipe: seqsfile

		frame (List)
			Frame(s) to translate -- Translation frames [select  values] (-frame)

		table (Excl)
			Code to use -- Genetic codes (-table)

		regions (Integer)
			Regions to translate (eg: 4-57,78-94) (-regions)

		trim (Switch)
			Trim trailing X's and *'s (-trim)

		alternative (Switch)
			Define frame '-1' as starting in the last codon (-alternative)

		outseq (OutFile)
			outseq (-outseq)
			pipe: seqsfile

		outseq_sformat (Excl)
			Output format for: outseq

		auto (String)

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• http://bioweb.pasteur.fr/seqanal/interfaces/transeq.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $transeq = Bio::Tools::Run::PiseApplication::transeq->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::transeq object.
          This method should not be used directly, but rather by 
          a Bio::Tools::Run::AnalysisFactory::Pise instance.
          my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
          my $transeq = $factory->program('transeq');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::transeq.