++ed by:
DEMIAN ILUX FIBO POTATOGIM PINGAN

11 PAUSE users
14 non-PAUSE users.

Christopher Fields
and 1 contributors

NAME

Bio::Tools::Seg - parse seg output

SYNOPSIS

  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";
    }
  }

DESCRIPTION

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.

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 the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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:

  http://bugzilla.open-bio.org/

AUTHOR - Torsten Seemann

Email - torsten.seemann AT infotech.monash.edu.au

CONTRIBUTOR - 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 _

new

 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

next_result

 Title   : next_result
 Usage   : my $feat = $seg->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::Generic
 Args    : none