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



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Module Version: 1.006924   Source  


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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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 of the bugs and their resolution. Bug reports can be submitted via the web:

AUTHOR - Torsten Seemann ^

Email - torsten.seemann AT


Email -


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
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