Christopher Fields > BioPerl-Run > Bio::Tools::Run::Seg

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BioPerl-Run-1.006900.tar.gz

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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
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