/ 
bioperl-run-1.2.2
/ Bio::Tools::Run::PiseApplication::lgicsearch

NAME

Bio::Tools::Run::PiseApplication::lgicsearch

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::lgicsearch

      Bioperl class for:

	LGIC	Search LGIC databases (Le Novere, Changeux)

	References:

		Nicolas LE NOVERE and Jean-Pierre CHANGEUX (1999). The Ligand-Gated Ion Channel database. Nucleic Acid Research, 27 : 340-342



      Parameters: 

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


		lgicsearch (Excl)
			Fasta program

		query (Sequence)
			Query sequence File

		seqtype (Excl)
			Is it a DNA or protein sequence

		protein_db (Excl)
			Protein Database

		nucleotid_db (Excl)
			Nucleotid Database

		ktup (Integer)

		threeframe (Switch)
			(tfasta only) only the three forward frames are searched

		txtoutput (String)

		lgicdbf2h (Switch)

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/MailList.shtml  - 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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

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/lgicsearch.html

  • Bio::Tools::Run::PiseApplication

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

  • Bio::Tools::Run::PiseJob

new

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