Bio::Tools::Run::PiseApplication::hmmbuild # Bio::Tools::Run::PiseApplication::hmmbuild Bioperl class for: HMMER hmmbuild - construct an HMM from a multiple sequence alignment (S. Eddy) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/hmmbuild.html for available values): hmmbuild (String) alignfile (Sequence) Aligned sequences File pipe: hmmer_alig hmmfile (OutFile) multiple_local (Switch) multiple local alignments (-f) single_global (Switch) single global alignment (-g) single_local (Switch) single local alignment (-s) name (String) name the HMM (-n 'name') re_save (OutFile) Re-save the starting alignment to 'file', in SELEX format. (-o 'file') append (InFile) append the model to an existing HMMs file (-A) amino (Switch) Force the sequence alignment to be interpreted as amino acid sequences. (--amino) archpri (Float) Set the 'architecture prior' to x (--archpri x) binary (Switch) Write the HMM to hmmfile in HMMER binary format instead of readable ASCII text. (--binary) cfile (Switch) Save the observed emission and transition counts to a file (--cfile f) fast (Switch) Quickly and heuristically determine the architecture of the model (--fast) gapmax (Float) Controls the --fast model construction algorithm, (--gapmax x) hand (Switch) Specify the architecture of the model by hand (--hand) idlevel (Float) (--idlevel x) noeff (Switch) Turn off the effective sequence number calculation (--noeff) nucleic (Switch) Force the alignment to be interpreted as nucleic acid sequence (--nucleic) null (InFile) null model (--null f) pam (InFile) heuristic PAM based prior (--pam f) pamwgt (Float) Controls the weight on a PAM-based prior. (--pamwgt x) pbswitch (Integer) PB weights (--pbswitch n) prior (InFile) Dirichlet prior (--prior f) swentry (Float) Controls the total probability that is distributed to local entries into the model (--swentry x) swexit (Float) Controls the total probability that is distributed to local exits from the model (--swexit x) verbose (Switch) Print more possibly useful stuff, such as the individual scores for each sequence in the alignment. (--verbose) wblosum (Switch) Use the BLOSUM filtering algorithm to weight the sequences (--wblosum) wgsc (Switch) Use the Gerstein/Sonnhammer/Chothia ad hoc sequence weighting algorithm. (--wgsc) wme (Switch) Use the Krogh/Mitchison maximum entropy algorithm to 'weight' the sequences. (--wme) wnone (Switch) Turn off all sequence weighting. (--wnone) wpb (Switch) Use the Henikoff position-based weighting scheme (--wpb) wvoronoi (Switch) Use the Sibbald/Argos Voronoi sequence weighting algorithm in place of the default GSC weighting. (--wvoronoi)

Mailing Lists
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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/hmmbuild.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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