/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::Genscan

NAME

Bio::Tools::Run::Genscan - Object for identifying genes in a given sequence given a matrix(for appropriate organisms).

SYNOPSIS

# 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);

DESCRIPTION

Genscan is a gene identifying program developed by Christopher Burge http://genes.mit.edu/burgelab/

By default it looks for an executable called genscan and data/parameter files in the directory specified by the GENSCANDIR environmental variable.

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

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.open-bio.org/

AUTHOR - Bala

Email savikalpa@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, 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    :