Bio::Tools::RNAMotif(3pm)				User Contributed Perl Documentation				 Bio::Tools::RNAMotif(3pm)

NAME

       Bio::Tools::RNAMotif - A parser for RNAMotif output

SYNOPSIS

	 use Bio::Tools::RNAMotif;
	 my $parser = Bio::Tools::RNAMotif->new(-file => $rna_output,
					       -motiftag => 'protein_bind'
					       -desctag => 'TRAP_binding');
	 #parse the results
	 while( my $motif = $parser->next_prediction) {
	   # do something here
	 }

DESCRIPTION

       Parses raw RNAMotif output.  RNAMotif uses a RNA profile, consisting of sequence and structural elements stored in a descriptor file, to
       search for potential motifs in a DNA sequence file.  For more information, see:

       Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R.	RNAMotif, an RNA secondary structure definition and search algorithm.
       Nucleic Acids Res. 2001 Nov 15;29(22):4724-35.  http://www.scripps.edu/mb/case/casegr-sh-3.5.html.

       This module is not currently complete.  As is, it will parse raw RNAMotif output (i.e. information not passed through the secondary
       programs rmfmt or rm2ct) and pack information into Bio::SeqFeature::Generic objects.  Currently, parsing extra output utilized by the
       sprintf() function in an RNAMotif descriptor is not implemented; this information is instead packed into the score tag, which can be
       accessed by using the following:

	 my ($score) = $feature->score;

       If the score contains anything besides a digit, it will throw a warning that sprintf() may have been used.  Several values have also been
       added in the 'tag' hash.  These can be accessed using the following syntax:

	 my ($entry) = $feature->get_Annotations('secstructure');

       Added tags are :

	  descline     - entire description line (in case the regex used for
			 sequence ID doesn't adequately catch the name
	  descfile     - name of the descriptor file (may include path to file)
	  secstrucure  - contains structural information from the descriptor
			 used as a query
	  sequence     - sequence of motif, separated by spaces according to
			 matches to the structure in the descriptor (in
			 SecStructure).

       See t/RNAMotif.t for example usage.

       The clean_features method can also be used to return a list of seqfeatures (in a Bio::SeqFeature::Collection object) that are within a
       particular region.   RNAMotif is prone with some descriptors to returning redundant hits; an attempt to rectify this problem is attempted
       with RNAMotif's companion program rmprune, which returns the structure with the longest helices (and theoretically the best scoring
       structure).  However, this doesn't take into account alternative foldings which may score better.  This method adds a bit more flexibility,
       giving the user the ability to screen folds based on where the feature is found and the score.  Passing a positive integer x screens
       SeqFeatures based on the highest score within x bp, while a negative integer screens based on the lowest score. So, to return the highest
       scoring values within 20 bp (likely using an arbitrary scroing system in the SCORE section of a descriptor file), one could use:

	 $list = $obj->clean_features(20);

       ... and returning the lowest scoring structures within the same region (when the score is based on calculated free energies from efn2) can
       be accomplished by the following:

	 $list = $obj->clean_features(-20);

       If you wanted the best feature in a sequence, you could set this to a large number, preferrably on that exceeds the bases in a sequence

	 $list = $obj->clean_features(10000000);

       Each seqfeature in the collection can then be acted upon:

	 @sf = $list->get_all_features;
	 for my $f (@sf) {
	   # do crazy things here
	 }

       At some point a more complicated feature object may be used to support this data rather than forcing most of the information into tag/value
       pairs in a SeqFeature::Generic.	This will hopefully allow for more flexible analysis of data (specifically RNA secondary structural data).
       It works for now...

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - Chris Fields
       Email cjfields-at-uiuc-dot-edu

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::RNAMotif->new();
	Function: Builds a new Bio::Tools::RNAMotif object
	Returns : an instance of Bio::Tools::RNAMotif
	Args	: -fh/-file for input filename
		  -motiftag => primary tag used in gene features (default 'misc_binding')
		  -desctag => tag used for display_name name (default 'rnamotif')
		  -srctag  => source tag used in all features (default 'RNAMotif')

   motif_tag
	Title	: motif_tag
	Usage	: $obj->motif_tag($newval)
	Function: Get/Set the value used for 'motif_tag', which is used for setting the
		  primary_tag.
		  Default is 'misc_binding' as set by the global $MotifTag.
		  'misc_binding' is used here because a conserved RNA motif is capable
		  of binding proteins (regulatory proteins), antisense RNA (siRNA),
		  small molecules (riboswitches), or nothing at all (tRNA,
		  terminators, etc.).  It is recommended that this be changed to other
		  tags ('misc_RNA', 'protein_binding', 'tRNA', etc.) where appropriate.
		  For more information, see:
		  http://www.ncbi.nlm.nih.gov/collab/FT/index.html
	Returns : value of motif_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   source_tag
	Title	: source_tag
	Usage	: $obj->source_tag($newval)
	Function: Get/Set the value used for the 'source_tag'.
		  Default is 'RNAMotif' as set by the global $SrcTag
	Returns : value of source_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   desc_tag
	Title	: desc_tag
	Usage	: $obj->desc_tag($newval)
	Function: Get/Set the value used for the query motif.  This will be placed in
		  the tag '-display_name'.  Default is 'rnamotif' as set by the global
		  $DescTag.  Use this to manually set the descriptor (motif searched for).
		  Since there is no way for this module to tell what the motif is from the
		  name of the descriptor file or the RNAMotif output, this should
		  be set every time an RNAMotif object is instantiated for clarity
	Returns : value of exon_tag (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   analysis_method
	Usage	  : $obj->analysis_method();
	Purpose   : Inherited method. Overridden to ensure that the name matches
		    /RNAMotif/i.
	Returns   : String
	Argument  : n/a

   next_feature
	Title	: next_feature
	Usage	: while($gene = $obj->next_feature()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the RNAMotif result
		  file. Call this method repeatedly until FALSE is returned.
		  The returned object is actually a SeqFeatureI implementing object.
		  This method is required for classes implementing the
		  SeqAnalysisParserI interface, and is merely an alias for
		  next_prediction() at present.
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	: None (at present)

   next_prediction
	Title	: next_prediction
	Usage	: while($gene = $obj->next_prediction()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the RNAMotif result
		  file. Call this method repeatedly until FALSE is returned.
	Returns : A Bio::SeqFeature::Generic object
	Args	: None (at present)

   clean_features
	Title	: next_prediction
	Usage	: @list = $obj->clean_features(-10);
	Function: Cleans (reduces redundant hits) based on score, position
	Returns : a Bio::SeqFeature::Collection object
	Args	: Pos./Neg. integer (for highest/lowest scoring seqfeature within x bp).
	Throws	: Error unless digit is entered.

perl v5.14.2							    2012-03-02						 Bio::Tools::RNAMotif(3pm)