use Bio::Tools::Run::Alignment::Exonerate;
  use Bio::SeqIO;

  my $qio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta');
  my $query = $qio->next_seq();
  my $tio = Bio::SeqIO->new(-file=>$ARGV[1],-format=>'fasta');
  my $target = $sio->next_seq();

  #exonerate parameters can all be passed via arguments parameter.
  #parameters passed are not checked for validity

  my $run = Bio::Tools::Run::Alignment::Exonerate->
      new(arguments=>'--model est2genome --bestn 10');
  my $searchio_obj = $run->run($query,$target);

  while(my $result = $searchio->next_result){
    while( my $hit = $result->next_hit ) {
      while( my $hsp = $hit->next_hsp ) {
        print $hsp->start."\t".$hsp->end."\n";


Wrapper for Exonerate alignment program. You can get exonerate at This wrapper is written without parameter checking. All parameters are passed via the arugment parameter that is passed in the constructor. See SYNOPSIS. For exonerate parameters, run exonerate --help for more details.


The tests have been shown to pass with exonorate versions 2.0 - 2.2.


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.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

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:

AUTHOR - Shawn Hoon



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
 Args    :


 Title   : new
 Usage   : my $factory= Bio::Tools::Run::Phrap->new();
 Function: creates a new Phrap factory
 Returns:  Bio::Tools::Run::Phrap
 Args    :


 Title   : version
 Usage   : exit if $prog->version() < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none


 Title   :   run()
 Usage   :   my $feats = $factory->run($seq)
 Function:   Runs Phrap 
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI


 Title   :   _input
 Usage   :   $factory->_input($seqFile)
 Function:   get/set for input file
 Returns :
 Args    :


 Title   :   _run
 Usage   :   $factory->_run()
 Function:   Makes a system call and runs Phrap
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :


 Title   :   _writeInput
 Usage   :   $factory->_writeInput($query,$target)
 Function:   Creates a file from the given seq object
 Returns :   A string(filename)
 Args    :   Bio::PrimarySeqI


 Title   :  _setparams
 Usage   :  Internal function, not to be called directly
 Function:  creates a string of params to be used in the command string
 Example :
 Returns :  string of params
 Args    :