--- name: "Bio::Tools::Run::Coil" section: "3pm" platform: "linux" package: "libbio-perl-run-perl" version: "1.7.3-13" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tools::Run::Coil" --- # Bio::Tools::Run::Coil(3pm) wrapper for ncoils program ## NAME Bio::Tools::Run::Coil - wrapper for ncoils program ## SYNOPSIS ``` # 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); ``` ## DESCRIPTION This module is a wrapper for the **ncoils** program available via \ 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. ## REFERENCES 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. ## 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 one of the Bioperl mailing lists. Your participation is much appreciated. ``` bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists ``` ### Support Please direct usage questions or support issues to the mailing list: *bioperl-l@bioperl.org* rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. ### Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: ``` http://redmine.open-bio.org/projects/bioperl/ ``` ## AUTHORS ``` Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil originally written by Marc Sohrmann (ms2@sanger.ac.uk) Written in BioPipe by Balamurugan Kumarasamy ``` \# Please direct questions and support issues to \ #\ Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org) ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ### program\_name ``` Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None ``` ### program\_dir ``` Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args : ``` ### new ``` Title : new Usage : $coil->new(@params) Function: creates a new Coil factory Returns: Bio::Tools::Run::Coil Args : ``` ### predict\_protein\_features ``` 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 ``` ### run ``` 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. ``` ### \_input ``` Title : _input Usage : obj->_input($seqFile) Function: Internal(not to be used directly) Returns : Args : ``` ### \_run ``` Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An array of Bio::SeqFeature::Generic objects Args : ``` ### \_writeSeqFile ``` Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal(not to be used directly) Returns : Args : ```