NAME

Bio::Tools::Run::PiseApplication::trimest

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::trimest

      Bioperl class for:

	TRIMEST	Trim poly-A tails off EST sequences (EMBOSS)


      Parameters: 

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


		trimest (String)

		init (String)

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

		minlength (Integer)
			Minimum length of a poly-A tail (-minlength)

		mismatches (Integer)
			Number of contiguous mismatches allowed in a tail (-mismatches)

		reverse (Switch)
			Write the reverse complement when poly-T is removed (-reverse)

		fiveprime (Switch)
			Remove poly-T tails at the 5' end of the sequence. (-fiveprime)

		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/trimest.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $trimest = Bio::Tools::Run::PiseApplication::trimest->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::trimest 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 $trimest = $factory->program('trimest');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::trimest.