Provided by: libbio-perl-perl_1.6.923-1_all 
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:
https://redmine.open-bio.org/projects/bioperl/
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