Bio::Search::HSP::HMMERHSP.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

     use Bio::Search::HSP::HMMERHSP;
     # us 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:
   http://bugzilla.open-bio.org/
 
 

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::Seach::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