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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

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.