Bio::Search::HSP::HMMERHSP - A HSP object for HMMER results use Bio::Search::HSP::HMMERHSP; # us it just like a Bio::Search::HSP::GenericHSP object This object is a specialization of Bio::Search::HSP::GenericHSP.

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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/ Email jason@bioperl.org Describe contact details here Additional contributors names and emails here 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::HMMERHSP(); 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 : $hsp->frame($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 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