NAME

Bio::Tools::Run::PiseApplication::blimps_matrix

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::blimps_matrix

      Bioperl class for:

	BLIMPS	score a block or matrix against a database of sequences (Wallace & Henikoff)

	References:

		J.C. Wallace and S. Henikoff, PATMAT: a searching and extraction program for sequence, pattern and block queries and databases, CABIOS, 8:3, p. 249-254 (1992).

		Steven Henikoff and Jorja G. Henikoff, Automated assembly of protein blocks for database searching, Nucleic Acids Research, 19:23, p. 6565-6572. (1991)



      Parameters: 

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


		blimps_matrix (String)

		action (String)

		sequence_db (Excl)
			Sequences database

		block_file (InFile)
			Block file

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

		matrix_file (InFile)
			A precomputed site specific scoring matrix file (instead of block file)

		genetic_code (Excl)
			The Genetic code to use (if DNA sequence or database)

		strands (Integer)
			The number of strands to search (if DNA sequence or database)

		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 (Integer)
			The number of scores to report.

		repeats (Switch)
			Repeats are allowed in the scoring list

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/blimps_matrix.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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