Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
Bio::Search::Hit::HitI objects should not be instantiated since this module defines a pure interface.
Given an object that implements the Bio::Search::Hit::HitI interface, you can do the following things with it:
$hit_name = $hit->name(); $desc = $hit->description(); $len = $hit->length $alg = $hit->algorithm(); $score = $hit->raw_score(); $significance = $hit->significance(); while( $hsp = $obj->next_hsp()) { ... } while( $hsp = $obj->next_hsp()) { ... }
Bio::Search::Hit::* objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined.
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Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
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Email amackey@virginia.edu (original author) Email sac@bioperl.org
Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights Reserved.
This software is provided "as is" without warranty of any kind.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : name Usage : $hit_name = $hit->name(); Function: returns the name of the Hit sequence Returns : a scalar string Args : none
Title : description Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string Args : none
Title : accession Usage : $acc = $hit->accession(); Function: Retrieve the accession (if available) for the hit Returns : a scalar string (empty string if not set) Args : none
Title : length Usage : my $len = $hit->length Function: Returns the length of the hit Returns : integer Args : none
Title : algorithm Usage : $alg = $hit->algorithm(); Function: Gets the algorithm specification that was used to obtain the hit For BLAST, the algorithm denotes what type of sequence was aligned against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated dna-prt, TBLASTN prt-translated dna, TBLASTX translated dna-translated dna). Returns : a scalar string Args : none
Title : raw_score Usage : $score = $hit->raw_score(); Function: Gets the "raw score" generated by the algorithm. What this score is exactly will vary from algorithm to algorithm, returning undef if unavailable. Returns : a scalar value Args : none
Title : significance Usage : $significance = $hit->significance(); Function: Used to obtain the E or P value of a hit, i.e. the probability that this particular hit was obtained purely by random chance. If information is not available (nor calculatable from other information sources), return undef. Returns : a scalar value or undef if unavailable Args : none
Title : next_hsp Usage : while( $hsp = $obj->next_hsp()) { ... } Function : Returns the next available High Scoring Pair Example : Returns : Bio::Search::HSP::HSPI object or null if finished Args : none
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.