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Manual Reference Pages  -  BIO::SEARCH::HSP::HMMERHSP (3)

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NAME

Bio::Search::HSP::HMMERHSP - A HSP object for HMMER results

CONTENTS

SYNOPSIS



    use Bio::Search::HSP::HMMERHSP;
    # use it just like a Bio::Search::HSP::GenericHSP object



DESCRIPTION

This object is a specialization of Bio::Search::HSP::GenericHSP.

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



AUTHOR - Jason Stajich

Email jason-at-bioperl.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::HMMERHSP->new();
 Function: Builds a new Bio::Search::HSP::HMMERHSP object
 Returns : Bio::Search::HSP::HMMERHSP
 Args    :



Plus Bio::Search::HSP::GenericHSP methods



    -algorithm    => algorithm used (BLASTP, TBLASTX, FASTX, 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)



    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



    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



    frac_identical



 Title   : frac_identical
 Usage   : my $frac_id = $hsp->frac_identical( [query|hit|total] );
 Function: Returns the fraction of identitical positions for this HSP
 Returns : Float in range 0.0 -> 1.0
 Args    : arg 1:  query = num identical / length of query seq (without gaps)
                   hit   = num identical / length of hit seq (without gaps)
                   total = num identical / length of alignment (with gaps)
                   default = total
           arg 2: [optional] frac identical value to set for the type requested



    frac_conserved



 Title    : frac_conserved
 Usage    : my $frac_cons = $hsp->frac_conserved( [query|hit|total] );
 Function : Returns the fraction of conserved positions for this HSP.
            This is the fraction of symbols in the alignment with a
            positive score.
 Returns : Float in range 0.0 -> 1.0
 Args    : arg 1: query = num conserved / length of query seq (without gaps)
                  hit   = num conserved / length of hit seq (without gaps)
                  total = num conserved / length of alignment (with gaps)
                  default = total
           arg 2: [optional] frac conserved value to set for the type requested



    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



    percent_identity



 Title   : percent_identity
 Usage   : my $percentid = $hsp->percent_identity()
 Function: Returns the calculated percent identity for an HSP
 Returns : floating point between 0 and 100
 Args    : none



    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



    num_conserved



 Title   : num_conserved
 Usage   : $obj->num_conserved($newval)
 Function: returns the number of conserved residues in the alignment
 Returns : inetger
 Args    : integer (optional)



    num_identical



 Title   : num_identical
 Usage   : $obj->num_identical($newval)
 Function: returns the number of identical residues in the alignment
 Returns : integer
 Args    : integer (optional)



    seq_inds



 Title   : seq_inds
 Purpose   : Get a list of residue positions (indices) for all identical
           : or conserved residues in the query or sbjct sequence.
 Example   : @s_ind = $hsp->seq_inds(query, identical);
           : @h_ind = $hsp->seq_inds(hit, conserved);
           : @h_ind = $hsp->seq_inds(hit, conserved, 1);
 Returns   : List of integers
           : May include ranges if collapse is true.
 Argument  : seq_type  = query or hit or sbjct  (default = query)
           :  (sbjct is synonymous with hit)
           : class     = identical or conserved or nomatch or gap
           :              (default = identical)
           :              (can be shortened to id or cons)
           :             
           : collapse  = boolean, if true, consecutive positions are merged
           :             using a range notation, e.g., "1 2 3 4 5 7 9 10 11"
           :             collapses to "1-5 7 9-11". This is useful for
           :             consolidating long lists. Default = no collapse.
 Throws    : n/a.
 Comments  :



See Also : Bio::Search::BlastUtils::collapse_nums(), Bio::Search::Hit::HitI::seq_inds()

    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



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perl v5.20.3 BIO::SEARCH::HSP::HMMERHSP (3) 2016-04-05

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