ncoils(1) [debian man page]
NCOILS(1) User Commands NCOILS(1) NAME
ncoils - prediction of coiled-coil secondary structure elements SYNOPSIS
ncoils [OPTION] < [FASTA FILE] ncoils -f < /usr/share/doc/ncoils/1srya.fa DESCRIPTION
ncoils is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. OPTIONS
-f, -fasta fasta output - coils as 'x', like '-x' in seg -c concise mode - which sequences have any coils (and how many) -min_seg <int> for concise mode - only report sequence if >= min coil segments -min_P <float> minimum P to define coil segment; DEFAULT = 0.5 -win <int> window size; DEFAULT = 21 -w weight heptad positions a&d the same as b,c,e,f,g -v verbose/debug mode - print extra junk EXAMPLES
"coils-wrap -m MTIDK -i /usr/share/doc/ncoils/1srya.fa -o /tmp/coils.out -r /tmp/coils_raw.txt && less /tmp/coils.out /tmp/coils_raw.txt" "ncoils -win 14 < /usr/share/doc/ncoils/1srya.fa" ENVIRONMENT
COILSDIR - specifies the directory containing the file new.mat overriding the default /usr/share/ncoils FILES
/usr/share/ncoils/*.mat matrix data files AUTHOR
R.B. Russell, A.N. Lupas COPYRIGHT AND LICENSE
GPL Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164 SEE ALSO
coils-wrap(1), "usr/share/doc/coils/README", http://www.russelllab.org/cgi-bin/coils/coils-svr.pl <http://www.russelllab.org/cgi- bin/coils/coils-svr.pl> A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996 A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991 2002 2011-10-29 NCOILS(1)
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Bio::Tools::Run::Coil(3pm) User Contributed Perl Documentation Bio::Tools::Run::Coil(3pm) 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 http://www.russell.embl-heidelberg.de/coils/coils.tar.gz <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. 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 <savikalpa@fugu-sg.org> # Please direct questions and support issues to <bioperl-l@bioperl.org> # 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 : perl v5.12.3 2011-06-18 Bio::Tools::Run::Coil(3pm)