Bio::Tools::Run::Seg - Object for identifying low complexity regions in a given protein seequence.
# 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);
Seg is a program which identifies low complexity regions in proteins. It was developed by Wootton and Federhen at NCBI.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory->program_name() Function: holds the program name Returns: string Args : None
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
Title : new Usage : $rm->new(@params) Function: creates a new Seg factory Returns: Bio::Tools::Run::Seg Args :
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
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
Title : _input Usage : obj->_input($seqFile) Function: Internal (not to be used directly) Returns : Args :
Title : _run Usage : $obj->_run() Function: Internal (not to be used directly) Returns : An array of Bio::SeqFeature::Generic objects Args : None
Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal (not to be used directly) Returns : string - Fasta filename to which $seq was written Args : Bio::Seq object