Bio::Tools::Run::Seg(3User Contributed Perl DocumentatiBio::Tools::Run::Seg(3)NAMEBio::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://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, 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
perl v5.14.1 2011-07-21 Bio::Tools::Run::Seg(3)
