Bio::Tools::Run::Pseudowise - Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence # Build a pseudowise alignment factory my $factory = Bio::Tools::Run::Pseudowise->new(); # Pass the factory 3 Bio:SeqI objects (in the order of query # peptide and cdna and target_genomic) # @genes is an array of GenericSeqFeature objects my @genes = $factory->run($seq1, $seq2, $seq3); Pseudowise is a pseudogene predition program developed by Ewan Birney http://www.sanger.ac.uk/software/wise2.

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 kiran@fugu-sg.org 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 instead Function: Predict pseudogenes Returns : An array of Bio::Seqfeature::Generic objects Args : Name of a file containing a set of 3 fasta sequences in the order of peptide, cdna and genomic sequences or else 3 Bio::Seq objects. Throws an exception if argument is not either a string (eg a filename) or 3 Bio::Seq objects. If arguments are strings, throws exception if file corresponding to string name can not be found.

run
Title : run Usage : my @feats = $factory->run($seq1, $seq2, $seq3); Function: Executes pseudogene binary Returns : An array of Bio::Seqfeature::Generic objects Args : Name of a file containing a set of 3 fasta sequences in the order of peptide, cdna and genomic sequences or else 3 Bio::Seq objects. Throws an exception if argument is not either a string (eg a filename) or 3 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 pseudowise program Example : Returns : nothing; pseudowise output is written to a temporary file $TMPOUTFILE Args : Name of a files containing 3 sequences in the order of peptide, cdna and genomic

_parse_results
Title : __parse_results Usage : Internal function, not to be called directly Function: Parses pseudowise output Example : Returns : an reference to an array of Seqfeatures Args : the name of the output file

_setinput()
Title : _setinput Usage : Internal function, not to be called directly Function: Create input files for pseudowise program Example : Returns : name of file containing dba data input Args : Seq objects in the order of query protein and cdna and target genomic sequence

_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 :

_query_cdna_seq()
Title : _query_cdna_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 :