Bio::Tools::Run::Genscan - Object for identifying genes in a given sequence given a matrix(for appropriate organisms). # Build a Genscan factory my $param = ('MATRIX'=>HumanIso.smat); my $factory = Bio::Tools::Run::Genscan->new($param); # Pass the factory a Bio::Seq object #@genes is an array of Bio::Tools::Predictions::Gene objects my @genes = $factory->run($seq); Genscan is a gene identifying program developed by Christopher Burge http://genes.mit.edu/burgelab/

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://bio.perl.org/MailList.html - About the mailing lists

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://bugzilla.bioperl.org/ Email savikalpa@fugu-sg.org 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, obtiained from ENV variable. Returns: string Args :

predict_genes()
Title : predict_genes() Usage : DEPRECATED: use $obj->run($seq) instead Function: Runs genscan and creates an array of Genes Returns : An array of Bio::Tools::Prediction::Gene objects Args : A Bio::PrimarySeqI

run
Title : run Usage : $obj->run($seq) Function: Runs genscan and creates an array of Genes Returns : An array of Bio::Tools::Prediction::Gene objects Args : A Bio::PrimarySeqI

_run
Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An array of Bio::Tools::Prediction::Gene objects Args :

_set_input()
Title : _set_input Usage : obj->_set_input($matrixFile,$seqFile) Function: Internal(not to be used directly) Returns : Args :

_writeSeqFile()
Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal(not to be used directly) Returns : Args :