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Bio::Tools::Run::Seg.3pm

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 low complexity region (in protein) identifying program developed by Wootton and Federhen at the National Center for Biotechnology Information (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://bio.perl.org/MailList.html             - 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.bioperl.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    :
 
 

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    :
 
 

_writeSeqFile

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