Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::Search::HSP::HMMEUser(Contributed Perl DocumBio::Search::HSP::HMMERHSP(3)

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

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

perl v5.24.1			  2017-07-08	 Bio::Search::HSP::HMMERHSP(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Search::HSP::HMMERHSP&sektion=3&manpath=FreeBSD+12.1-RELEASE+and+Ports>

home | help