Bio::Tools::Run::GenscUser)Contributed Perl DocumenBio::Tools::Run::Genscan(3)NAMEBio::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://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, 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 :
perl v5.14.1 2011-07-21 Bio::Tools::Run::Genscan(3)
