NAME

Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences using promoterwise

SYNOPSIS

  # Build a Promoterwise alignment factory
  my @params = ('-s'=>1,'-query_start'=>10,'-dymem'=>1);
  my  $factory = Bio::Tools::Run::Promoterwise->new(@params);

  my (@fp)= $factory->run($seq1,$seq2);

  # each feature pair is a group of hsps
  foreach my $fp(@fp){
    print "Hit Length: ".$fp->feature1->length."\n";
    print "Hit Start: ".$fp->feature1->start."\n";
    print "Hit End: ".$fp->feature1->end."\n";
    print "Hsps: \n";
    my @first_hsp = $fp->feature1->sub_SeqFeature;
    my @second_hsp = $fp->feature2->sub_SeqFeature;
    for ($i..$#first_hsp){
      print $first_hsp[$i]->seq." ".$second_hsp[$i]->seq."\n";
    }
  }
  print "end: ". $fp->feature2->start."\t".$fp->feature2->end."\n";

  #Available parameters include:
  #( S T U V QUERY_START QUERY_END TARGET_START
  #TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT
  #LHREJECT LHMAX DYMEM KBYTE DYCACHE)
  #For an explanation of these parameters, please see documentation
  #from the Wise package.

DESCRIPTION

Promoterwise is an alignment algorithm that relaxes the constraint that local alignments have to be co-linear. Otherwise it provides a similar model to DBA, which is designed for promoter sequence alignments by Ewan Birney. It is part of the wise2 package available at: http://www.sanger.ac.uk/software/wise2.

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 one of the Bioperl mailing lists. Your participation is much appreciated.

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

Support

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

bioperl-l@bioperl.org

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:

  http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Shawn Hoon

Email: shawnh@fugu-sg.org

APPENDIX

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

program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

program_dir

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :

version

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

run

 Title   : run 
 Usage   : 2 sequence objects
           @fp = $factory->run($seq1, $seq2);
 Function: run 
 Returns : An array of <Bio::SeqFeature::FeaturePair> 
 Args    : Name of a file containing a set of 2 fasta sequences 
           or else 2  Bio::Seq objects.

Throws an exception if argument is not either a string (eg a filename) or 2 Bio::Seq objects. If arguments are strings, throws exception if file corresponding to string name can not be found.

_run

 Title   :  _run
 Usage   :  Internal function, not to be called directly
 Function:   makes actual system call to a promoterwise program
 Example :
 Returns : L<Bio::SeqFeature::FeaturePair>
 Args    : Name of a files containing 2 sequences in the order of peptide and genomic

_setparams

 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    :

_query_pep_seq

 Title   :  _query_pep_seq
 Usage   :  Internal function, not to be called directly
 Function:  get/set for the query sequence
 Example :
 Returns :  
 Args    :

_subject_dna_seq

 Title   :  _subject_dna_seq
 Usage   :  Internal function, not to be called directly
 Function:  get/set for the subject sequence
 Example :
 Returns :

 Args    :