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

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/

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, obtained 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    :