Bio::Tools::Run::PiseApplication::sigscan # Bio::Tools::Run::PiseApplication::sigscan Bioperl class for: SIGSCAN Scans a sparse protein signature against swissprot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/sigscan.html for available values): sigscan (String) init (String) sigin (InFile) Name of signature file for input (-sigin) database (Sequence) Name of sequence database to search (-database) pipe: seqsfile targetf (InFile) Name of (optionally grouped) scop families file for input (-targetf) thresh (Integer) Minimum length (residues) of overlap required for two hits with the same code to be counted as the same hit. (-thresh) sub (Excl) Residue substitution matrix (-sub) gapo (Float) Gap insertion penalty (-gapo) gape (Float) Gap extension penalty (-gape) nterm (Excl) Select number -- N-terminal matching options (-nterm) nhits (Integer) Number of hits to output (-nhits) hitsf (OutFile) Name of signature hits file for output (-hitsf) alignf (OutFile) Name of signature alignments file for output (-alignf) auto (String)

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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.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) 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. This software is provided "as is" without warranty of any kind. http://bioweb.pasteur.fr/seqanal/interfaces/sigscan.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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