Bio::Tools::Run::Genewise(3pm)				User Contributed Perl Documentation			    Bio::Tools::Run::Genewise(3pm)

NAME

       Bio::Tools::Run::Genewise - Object for predicting genes in a given sequence given a protein

SYNOPSIS

	 # Build a Genewise alignment factory
	 my $factory = Bio::Tools::Run::Genewise->new();

	 # Pass the factory 2 Bio:SeqI objects (in the order of query peptide
	 # and target_genomic).

	 # @genes is an array of Bio::SeqFeature::Gene::GeneStructure objects
	 my @genes = $factory->run($protein_seq, $genomic_seq);

	 # Alternatively pass the factory a profile HMM filename and a
	 # Bio:SeqI object (in the order of query HMM and target_genomic).

	 # Set hmmer switch first to tell genewise to expect an HMM
	 $factory->hmmer(1);
	 my @genes = $factory->run($hmmfile, $genomic_seq);

DESCRIPTION

       Genewise is a gene prediction program developed by Ewan Birney http://www.sanger.ac.uk/software/wise2.

   Available Params:
       NB: These should be passed without the '-' or they will be ignored, except switches such as 'hmmer' (which have no corresponding value)
       which should be set on the factory object using the AUTOLOADed methods of the same name.

	 Model	  [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null]
	 Alg	  [-kbyte,-alg]
	 HMM	  [-hmmer]
	 Output   [-gff,-gener,-alb,-pal,-block,-divide]
	 Standard [-help,-version,-silent,-quiet,-errorlog]

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 - FUGU Student Intern
       Email: fugui@worf.fugu-sg.org

CONTRIBUTORS

       Jason Stajich jason-AT-bioperl_DOT_org Keith James kdj@sanger.ac.uk

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

   predict_genes
	Title	: predict_genes
	Usage	: DEPRECATED. Use $factory->run($seq1,$seq2)
	Function: Predict genes
	Returns : A Bio::Seqfeature::Gene:GeneStructure object
	Args	: Name of a file containing a set of 2 fasta sequences in the order of
		  peptide and genomic 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	: 2 sequence objects
		  $genes = $factory->run($seq1, $seq2);
	Function: run
	Returns : A Bio::Seqfeature::Gene:GeneStructure object
	Args	: Names of a files each containing a fasta sequence in the order
		  of either (peptide sequence, genomic sequence) or (profile HMM,
		  genomic sequence). Alternatively any of the fasta sequence
		  filenames may be substituted with a Bio::Seq object.

       Throws an exception if argument is not either a string (eg a filename) or Bio::Seq objects. If arguments are strings, throws exception if
       file corresponding to string name can not be found. Also throws an exception if a profile HMM is expected (the -hmmer genewise switch has
       been set).

   _run
	Title	: _run
	Usage	: Internal function, not to be called directly
	Function: Makes actual system call to a genewise program
	Example :
	Returns : L<Bio::SeqFeature::Gene::GeneStructure>
	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	:

perl v5.12.3							    2011-06-18					    Bio::Tools::Run::Genewise(3pm)