Bio::Search::HSP::ModelHSP(3)

NAME
Bio::Search::HSP::ModelHSP - A HSP object for model-based searches

SYNOPSIS
    use Bio::Search::HSP::ModelHSP;
    # us it just like a Bio::Search::HSP::ModelHSP object

DESCRIPTION
This object is a specialization of Bio::Search::HSP::ModelHSP and is used for searches which involve a query model, such as a Hidden Markov Model (HMM), covariance model (CM), descriptor, or anything else besides a sequence. Note that results from any HSPI class methods which rely on the query being a sequence are unreliable and have thus been overridden with warnings indicating they have not been implemented at this time.

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:

  http://bugzilla.open-bio.org/

AUTHOR - Chris Fields
Email cjfields at bioperl dot org

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::Search::HSP::ModelHSP->new();
 Function: Builds a new Bio::Search::HSP::ModelHSP object
 Returns : Bio::Search::HSP::ModelHSP
 Args    :

Plus Bio::Seach::HSP::ModelHSP methods

           -algorithm => algorithm used (Infernal, RNAMotif, ERPIN, etc)
           -evalue    => evalue
           -pvalue    => pvalue
           -bits      => bit value for HSP
           -score     => score value for HSP (typically z-score but depends on
                                              analysis)
           -hsp_length=> Length of the HSP (including gaps)
           -identical => # of residues that that matched identically
           -conserved => # of residues that matched conservatively
                           (only protein comparisions;
                            conserved == identical in nucleotide comparisons)
           -hsp_gaps   => # of gaps in the HSP
           -query_gaps => # of gaps in the query in the alignment
           -hit_gaps   => # of gaps in the subject in the alignment
           -query_name  => HSP Query sequence name (if available)
           -query_start => HSP Query start (in original query sequence coords)
           -query_end   => HSP Query end (in original query sequence coords)
           -hit_name    => HSP Hit sequence name (if available)
           -hit_start   => HSP Hit start (in original hit sequence coords)
           -hit_end     => HSP Hit end (in original hit sequence coords)
           -hit_length  => total length of the hit sequence
           -query_length=> total length of the query sequence
           -query_seq   => query sequence portion of the HSP
           -hit_seq     => hit sequence portion of the HSP
           -homology_seq=> homology sequence for the HSP
           -hit_frame   => hit frame (only if hit is translated protein)
           -query_frame => query frame (only if query is translated protein)
           -meta        => optional meta data (sec structure, markup, etc)
           -custom_score=> custom score data

  meta
 Title   : meta
 Usage   : my $meta = $hsp->meta();
 Function: Returns meta data for this HSP or undef
 Returns : string of meta data or undef
 Args    : [optional] string to set value
 Note    : At some point very soon this will likely be a Bio::AnnotationI.
           Don't get used to a simple string!

  custom_score
 Title   : custom_score
 Usage   : my $data = $hsp->custom_score();
 Function: Returns custom_score data for this HSP, or undef
 Returns : custom_score data or undef
 Args    : [optional] custom_score
 Note    : This is a Get/Set used to deal with odd score-like data generated
           from RNAMotif (and other programs) where the score section
           can be customized to include non-standard data, including sequence
           data, user-based scores, and other values.

  Bio::Search::HSP::HSPI methods
Implementation of Bio::Search::HSP::HSPI methods follow

  algorithm
 Title   : algorithm
 Usage   : my $r_type = $hsp->algorithm
 Function: Obtain the name of the algorithm used to obtain the HSP
 Returns : string (e.g., BLASTP)
 Args    : [optional] scalar string to set value

  strand
 Title   : strand
 Usage   : $hsp->strand('hit')
 Function: Retrieves the strand for the HSP component requested
 Returns : +1 or -1 (0 if unknown)
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject.
           There is no strand available for 'query', as the query is a model
           and not a true sequence.

  seq
 Usage     : $hsp->seq( [seq_type] );
 Purpose   : Get the query or sbjct sequence as a Bio::Seq.pm object.
 Example   : $seqObj = $hsp->seq('sbjct');
 Returns   : Object reference for a Bio::Seq.pm object.
 Argument  : seq_type = 'query' or 'hit' or 'sbjct' (default = 'sbjct').
           :  ('sbjct' is synonymous with 'hit')
           : default is 'sbjct'
           : Note: if there is no sequence available (eg for a model-based
           : search), this returns a LocatableSeq object w/o a sequence
 Throws    : Propagates any exception that occurs during construction
           : of the Bio::Seq.pm object.
 Comments  : The sequence is returned in an array of strings corresponding
           : to the strings in the original format of the Blast alignment.
           : (i.e., same spacing).

See Also : seq_str(), Bio::Seq

  pvalue
 Title   : pvalue
 Usage   : my $pvalue = $hsp->pvalue();
 Function: Returns the P-value for this HSP or undef
 Returns : float or exponential (2e-10)
           P-value is not defined with NCBI Blast2 reports.
 Args    : [optional] numeric to set value

  evalue
 Title   : evalue
 Usage   : my $evalue = $hsp->evalue();
 Function: Returns the e-value for this HSP
 Returns : float or exponential (2e-10)
 Args    : [optional] numeric to set value

  gaps
 Title    : gaps
 Usage    : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
 Function : Get the number of gaps in the query, hit, or total alignment.
 Returns  : Integer, number of gaps or 0 if none
 Args     : arg 1: 'query' = num gaps in query seq
                   'hit'   = num gaps in hit seq
                   'total' = num gaps in whole alignment
                   default = 'total'
            arg 2: [optional] integer gap value to set for the type requested

  query_string
 Title   : query_string
 Usage   : my $qseq = $hsp->query_string;
 Function: Retrieves the query sequence of this HSP as a string
 Returns : string
 Args    : [optional] string to set for query sequence

  hit_string
 Title   : hit_string
 Usage   : my $hseq = $hsp->hit_string;
 Function: Retrieves the hit sequence of this HSP as a string
 Returns : string
 Args    : [optional] string to set for hit sequence

  homology_string
 Title   : homology_string
 Usage   : my $homo_string = $hsp->homology_string;
 Function: Retrieves the homology sequence for this HSP as a string.
         : The homology sequence is the string of symbols in between the
         : query and hit sequences in the alignment indicating the degree
         : of conservation (e.g., identical, similar, not similar).
 Returns : string
 Args    : [optional] string to set for homology sequence

  length
 Title    : length
 Usage    : my $len = $hsp->length( ['query'|'hit'|'total'] );
 Function : Returns the length of the query or hit in the alignment
            (without gaps)
            or the aggregate length of the HSP (including gaps;
            this may be greater than either hit or query )
 Returns  : integer
 Args     : arg 1: 'query' = length of query seq (without gaps)
                   'hit'   = length of hit seq (without gaps)
                   'total' = length of alignment (with gaps)
                   default = 'total'
            arg 2: [optional] integer length value to set for specific type

  frame
 Title   : frame
 Usage   : my ($qframe, $hframe) = $hsp->frame('list',$queryframe,$subjectframe)
 Function: Set the Frame for both query and subject and insure that
           they agree.
           This overrides the frame() method implementation in
           FeaturePair.
 Returns : array of query and subject frame if return type wants an array
           or query frame if defined or subject frame if not defined
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default)
           'query' to retrieve the query frame
           'list' or 'array' to retrieve both query and hit frames together
 Note    : Frames are stored in the GFF way (0-2) not 1-3
           as they are in BLAST (negative frames are deduced by checking
                                 the strand of the query or hit)

  get_aln
 Title   : get_aln
 Usage   : my $aln = $hsp->gel_aln
 Function: Returns a Bio::SimpleAlign representing the HSP alignment
 Returns : Bio::SimpleAlign
 Args    : none

  Inherited from Bio::SeqFeature::SimilarityPair
These methods come from Bio::SeqFeature::SimilarityPair

  query
 Title   : query
 Usage   : my $query = $hsp->query
 Function: Returns a SeqFeature representing the query in the HSP
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] new value to set

  hit
 Title   : hit
 Usage   : my $hit = $hsp->hit
 Function: Returns a SeqFeature representing the hit in the HSP
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] new value to set

  significance
 Title   : significance
 Usage   : $evalue = $obj->significance();
           $obj->significance($evalue);
 Function: Get/Set the significance value
 Returns : numeric
 Args    : [optional] new value to set

  score
 Title   : score
 Usage   : my $score = $hsp->score();
 Function: Returns the score for this HSP or undef
 Returns : numeric
 Args    : [optional] numeric to set value

  bits
 Title   : bits
 Usage   : my $bits = $hsp->bits();
 Function: Returns the bit value for this HSP or undef
 Returns : numeric
 Args    : none

ModelHSP methods overridden in ModelHSP
The following methods have been overridden due to their current reliance on sequence-based queries. They may be implemented in future versions of this class.

  seq_inds

  frac_identical

  frac_conserved

  matches

  num_conserved

  num_identical

  cigar_string

  generate_cigar_string

  percent_identity