Man pages sections > man3 > Bio::Tools::Seg

Bio::Tools::Seg - parse "seg" output

Bio::Tools::Seg(3pm) User Contributed Perl Documentation Bio::Tools::Seg(3pm)


Bio::Tools::Seg - parse "seg" output


  use Bio::Tools::Seg;
  my $parser = Bio::Tools::Seg->(-file => 'seg.fasta');
  while ( my $f = $parser->next_result ) {
    if ($f->score < 1.5) {
      print $f->location->to_FTstring, " is low complexity\n";


"seg" identifies low-complexity regions on a protein sequence. It is usually part of the "WU-BLAST" and "InterProScan" packages.
The Bio::Tools::Seg module will only parse the "fasta" output modes of "seg", i.e. "seg -l" (low complexity regions only), "seg -h" (high complexity regions only), or "seg -a" (both low and high).
It creates a Bio::SeqFeature::Generic for each FASTA-like entry found in the input file. It is up to the user to appropriately filter these using the feature's score.


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AUTHOR - Torsten Seemann

Email - torsten.seemann AT


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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $obj = Bio::Tools::Seg->new();
 Function: Builds a new Bio::Tools::Seg object
 Returns : Bio::Tools::Seg
 Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO


 Title   : next_result
 Usage   : my $feat = $seg->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::Generic
 Args    : none
2017-08-30 perl v5.26.0