NAME

Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair

SYNOPSIS

my $hsp = new Bio::Search::HSP::GenericHSP( -algorithm => 'blastp',
                                            -evalue    => '1e-30',
                                            );

$r_type = $hsp->algorithm;

$pvalue = $hsp->p();

$evalue = $hsp->evalue();

$frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );

$frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );

$gaps = $hsp->gaps( ['query'|'hit'|'total'] );

$qseq = $hsp->query_string;

$hseq = $hsp->hit_string;

$homo_string = $hsp->homology_string;

$len = $hsp->length( ['query'|'hit'|'total'] );

$len = $hsp->length( ['query'|'hit'|'total'] );

$rank = $hsp->rank;

# TODO: Describe how to configure a SearchIO stream so that it generates # GenericHSP objects.

DESCRIPTION

This implementation is "Generic", meaning it is is suitable for holding information about High Scoring pairs from most Search reports such as BLAST and FastA. Specialized objects can be derived from this.

Unless you're writing a parser, you won't ever need to create a GenericHSP or any other HSPI-implementing object. If you use the SearchIO system, HSPI objects are created automatically from a SearchIO stream which returns Bio::Search::Result::ResultI objects and you get the HSPI objects via the ResultI API.

For documentation on what you can do with GenericHSP (and other HSPI objects), please see the API documentation in Bio::Search::HSP::HSPI.

FEEDBACK

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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/MailList.shtml  - About the mailing lists

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 email or the web:

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich and Steve Chervitz

Email jason@bioperl.org Email sac@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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 = new Bio::Search::HSP::GenericHSP();
Function: Builds a new Bio::Search::HSP::GenericHSP object 
Returns : Bio::Search::HSP::GenericHSP
Args    : -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
          -percent_identity => (optional) percent identity
          -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)
          -rank        => HSP rank
          -links       => HSP links information (WU-BLAST only)

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)
                            synonyms: 'sbjct', 'subject'
                  'total' = num conserved / length of alignment (with gaps)
                            synonyms: 'hsp'
                  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)
                            synonyms: 'sbjct', 'subject'
                 'total' = num conserved / length of alignment (with gaps)
                            synonyms: 'hsp'
                 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; synonyms: 'sbjct', 'subject'
                  'total' = num gaps in whole alignment;  synonyms: 'hsp'
                  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) (synonyms: sbjct, subject)
                  'total' = length of alignment (with gaps)
                  default = 'total' 
           arg 2: [optional] integer length value to set for specific type

hsp_length

Title   : hsp_length
Usage   : my $len = $hsp->hsp_length()
Function: shortcut  length('hsp')
Returns : floating point between 0 and 100 
Args    : none

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   : $hsp->frame($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 subjects if return type wants an array
          or query frame if defined or subject frame
Args    : none
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 L<Bio::SimpleAlign> object representing the HSP alignment
Returns : L<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)

rank

Usage     : $hsp->rank( [string] );
Purpose   : Get the rank of the HSP within a given Blast hit.
Example   : $rank = $hsp->rank;
Returns   : Integer (1..n) corresponding to the order in which the HSP
            appears in the BLAST report.

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-not-identical'); 
          : @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')
          :             or 'conserved-not-identical'
          : 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  :

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 : L<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 : L<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

bits

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

strand

Title   : strand
Usage   : $hsp->strand('query')
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
          'query' to retrieve the query strand (default)

Private methods

_calculate_seq_positions

Title   : _calculate_seq_positions
Usage   : $self->_calculate_seq_positions
Function: Internal function
Returns : 
Args    :

n

See documentation in Bio::Search::HSP::HSPI::n()

range

See documentation in Bio::Search::HSP::HSPI::range()

links

Title   : links
Usage   : $obj->links($newval)
Function: Get/Set the Links value (from WU-BLAST)
          Indicates the placement of the alignment in the group of HSPs
Returns : Value of links
Args    : On set, new value (a scalar or undef, optional)

Brief introduction on cigar string

NOTE: the concept is originally from EnsEMBL docs at http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/CigarFormat.html. Please append to these docs if you have a better definition.

Sequence alignment hits can be stored in a database as ungapped alignments. This imposes 2 major constraints on alignments:

a) alignments for a single hit record require multiple rows in the database, and b) it is not possible to accurately retrieve the exact original alignment.

Alternatively, sequence alignments can be stored as gapped alignments using the CIGAR line format (where CIGAR stands for Concise Idiosyncratic Gapped Alignment Report).

In the cigar line format alignments are stored as follows:

M: Match D: Deletion I: Insertion

An example of an alignment for a hypthetical protein match is shown below:

Query: 42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...

PG    P    G     GP   R      PLGP

Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...

protein_align_feature table as the following cigar line:

7M4D12M2I2MD7M

cigar_string

Name:     cigar_string
Usage:    $cigar_string = $hsp->cigar_string
Function: Generate and return cigar string for this HSP alignment
Args:     No input needed
Return:   a cigar string

generate_cigar_string

Name:     generate_cigar_string
Usage:    my $cigar_string = Bio::Search::HSP::GenericHSP::generate_cigar_string ($qstr, $hstr);
Function: generate cigar string from a simple sequence of alignment.
Args:     the string of query and subject
Return:   cigar string

To install Bio::Seq, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Seq

CPAN shell

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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