Bio::Tools::Run::Coil - wrapper for ncoils program
# Build a Coil factory my $factory = Bio::Tools::Run::Coil->new($params); # Pass the factory a Bio::Seq object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq);
This module is a wrapper for the ncoils program available via http://www.russell.embl-heidelberg.de/coils/coils.tar.gz for predicting coiled coils in protein sequences.
By default it looks for an executable called ncoils and data/parameter files in the directory specified by the COILSDIR environmental variable.
Lupas, van Dyke & Stock, Predicting coiled coils from protein sequences, Science 252:1162-1164, 1991.
Lupas, A., Prediction and Analysis of Coiled-Coil Structures, Meth. Enzymology 266:513-525, 1996.
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Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil originally written by Marc Sohrmann (firstname.lastname@example.org) Written in BioPipe by Balamurugan Kumarasamy <email@example.com>
# Please direct questions and support issues to <firstname.lastname@example.org> # Cared for by the Fugu Informatics team (email@example.com)
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
Title : new Usage : $coil->new(@params) Function: creates a new Coil factory Returns: Bio::Tools::Run::Coil Args :
Title : predict_protein_features() Usage : DEPRECATED. Use $obj->run instead. Function: Runs Coil and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI
Title : run Usage : $obj->run($seq) Function: Runs Coil and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI, or a Fasta filename.
Title : _input Usage : obj->_input($seqFile) Function: Internal(not to be used directly) Returns : Args :
Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An array of Bio::SeqFeature::Generic objects Args :
Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal(not to be used directly) Returns : Args :