/ 
bioperl-run-1.5.2_100
/ Bio::Tools::Run::Promoterwise

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

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://bugzilla.open-bio.org/

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, obtiained 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    :