/ 
bioperl-run-1.4
/ Bio::Tools::Run::PiseApplication::blimps

NAME

Bio::Tools::Run::PiseApplication::blimps

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::blimps

      Bioperl class for:

	BLIMPS	BLocks IMProved Searcher (Wallace, Henikoff)


      Parameters: 

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


		blimps (String)

		action (Excl)
			Action

		blocks_db (Excl)
			Blocks database

		sequence_file (Sequence)
			Sequence file filename to score against blocks database

		sequence_db (Excl)
			Sequences database

		block_file (InFile)
			Block file filename

		matrix_file (InFile)
			A precomputed site specific scoring matrix file

		conversion (Excl)
			Conversion method for converting a block to a matrix

		genetic_code (Excl)
			The Genetic code to use

		strand (Switch)
			both strands to be searched

		outfile (OutFile)
			Output file filename

		error (Excl)
			Error level to report at

		export_matrix (OutFile)
			Export matrix (matricies) to this filename

		histogram (Switch)
			Print the histogram values in the output file

		scores_number (Integer)
			The number of scores to report.

		repeats (Switch)
			Repeats are allowed in the scoring list

		error_file (OutFile)

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/blimps.html

  • Bio::Tools::Run::PiseApplication

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

  • Bio::Tools::Run::PiseJob

new

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