- AUTHOR - Bala
Bio::Tools::Run::Seg - Object for identifying low complexity regions in a given protein seequence.
# Build a Seg factory # $paramfile is the full path to the seg binary file my @params = ('PROGRAM',$paramfile); my $factory = Bio::Tools::Run::Seg->new($param); # Pass the factory a Bio::Seq object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq);
Seg is a program which identifies low complexity regions in proteins. It was developed by Wootton and Federhen at NCBI.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
AUTHOR - Bala
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, or undef if $SEGDIR not in ENV Args : None
Title : new Usage : $rm->new(@params) Function: creates a new Seg factory Returns: Bio::Tools::Run::Seg Args :
Title : predict_protein_features() Usage : DEPRECATED Use $obj->run($seq) instead Function: Runs Seg 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 Seg and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI
Title : _input Usage : obj->_input($seqFile) Function: Internal (not to be used directly) Returns : Args :
Title : _run Usage : $obj->_run() Function: Internal (not to be used directly) Returns : An array of Bio::SeqFeature::Generic objects Args : None
Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal (not to be used directly) Returns : string - Fasta filename to which $seq was written Args : Bio::Seq object