Bio::Tools::Run::Genewise - Object for predicting genes in a given sequence given a protein # 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); 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]

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://bio.perl.org/MailList.html - 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.bioperl.org/ Email: fugui@worf.fugu-sg.org Jason Stajich jason@bioperl.org Keith James kdj@sanger.ac.uk 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

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 :