Provided by: libbio-perl-perl_1.6.923-1_all bug


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


         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


       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

       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

       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...


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       of the problem with code and data examples if at all possible.

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AUTHOR - Chris Fields

       Email cjfields-at-uiuc-dot-edu


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

        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')

        Title   : motif_tag
        Usage   : $obj->motif_tag($newval)
        Function: Get/Set the value used for 'motif_tag', which is used for setting the
                  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:
        Returns : value of motif_tag (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

        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)

        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)

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

        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)

        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)

        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.