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Bio::Search::HSP::ModeUser(Contributed Perl DocumBio::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:

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

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	comparisons;
				   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!

   noncanonical_string
	Title	: noncanonical_string
	Usage	: my $nc_seq = $hsp->noncanonical_string();
	Function: Returns noncanonical string (NC) data	for this HSP or	undef
	Returns	: string of noncanonical data or undef
	Args	: [optional] string to set value

   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
perl v5.32.0			  2019-12-07	 Bio::Search::HSP::ModelHSP(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chris Fields | APPENDIX | ModelHSP methods overridden in ModelHSP

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