/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Seg

NAME

Bio::Tools::Run::Seg - Object for identifying low complexity regions in a given protein seequence.

SYNOPSIS

# 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);

DESCRIPTION

Seg is a program which identifies low complexity regions in proteins. It was developed by Wootton and Federhen at NCBI.

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, or undef if $SEGDIR not in ENV
Args    : None

new

Title   : new
Usage   : $rm->new(@params)
Function: creates a new Seg factory
Returns:  Bio::Tools::Run::Seg
Args    :

predict_protein_features

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

run

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

_input

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

_run

Title   :   _run
Usage   :   $obj->_run()
Function:   Internal (not to be used directly)
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :   None

_writeSeqFile

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