Search results for "dist:BioPerl Bio::Search::HSP::HSPI"
Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result
Bio::Search::HSP::HSPI objects cannot be instantiated since this module defines a pure interface. Given an object that implements the Bio::Search::HSP::HSPI interface, you can do the following things with it:...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::PullHSPI - Bio::Search::HSP::HSPI interface for pull parsers.
PullHSP is for fast implementations that only do parsing work on the hsp data when you actually request information by calling one of the HSPI methods. Many methods of HSPI are implemented in a way suitable for inheriting classes that use Bio::PullPa...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Tiling::MapTileUtils - utilities for manipulating closed intervals for an HSP tiling algorithm
Not used directly....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects
This is a general way of hiding the object creation process so that we can dynamically change the objects that are created by the SearchIO parser depending on what format report we are parsing. This object is for creating new HSPs....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::Writer::HSPTableWriter - Tab-delimited data for Bio::Search::HSP::HSPI objects
Bio::SearchIO::Writer::HSPTableWriter generates output at the finest level of granularity for data within a search result. Data for each HSP within each hit in a search result is output in tab-delimited format, one row per HSP. Available Columns Here...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
This is a driver for instantiating a parser for report files from sequence database searches. This object serves as a wrapper for the format parsers in Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For people used...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::PullHitI - Bio::Search::Hit::HitI interface for pull parsers.
This object handles the hit data from a database sequence search. PullHitI is for fast implementations that only do parsing work on the hit data when you actually request information by calling one of the HitI methods. Many methods of HitI are implem...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::ModelHSP - A HSP object for model-based searches
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 an...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
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....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::ModelHit - A model-based implementation of the Bio::Search::Hit::HitI interface
This object handles the hit data from a database search using models or descriptors instead of sequences, such as Infernal, HMMER, RNAMotif, etc. Unless you're writing a parser, you won't ever need to create a ModelHit or any other HitI-implementing ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI interface
This object handles the hit data from a Database Sequence Search such as FASTA or BLAST. Unless you're writing a parser, you won't ever need to create a GenericHit or any other HitI-implementing object. If you use the SearchIO system, HitI objects ar...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module
This module provides strong suggestions for any intended HSP tiling object implementation. An object subclassing TilingI should override the methods defined here according to their descriptions below. See the section STATISTICS METHODS for hints on i...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps
This object implements a parser for BlastN hsp output....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing
This interface describes the basic methods needed to handle Events thrown from parsing a Search Result such as FASTA, BLAST, or HMMer....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::BlastHSP - Bioperl BLAST High-Scoring Pair object
A Bio::Search::HSP::BlastHSP object provides an interface to data obtained in a single alignment section of a Blast report (known as a "High-scoring Segment Pair"). This is essentially a pairwise alignment with score information. BlastHSP objects are...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair
This implementation is "Generic", meaning it is is suitable for holding information about High Scoring pairs from most Search reports such as BLAST and FastA. Specialized objects can be derived from this. Unless you're writing a parser, you won't eve...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Tiling::MapTiling - An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics
Frequently, users want to use a set of high-scoring pairs (HSPs) obtained from a BLAST or other search to assess the overall level of identity, conservation, or coverage represented by matches between a subject and a query sequence. Because a set of ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::PsiBlastHSP - Bioperl BLAST High-Scoring Pair object
A Bio::Search::HSP::PsiBlastHSP object provides an interface to data obtained in a single alignment section of a Blast report (known as a "High-scoring Segment Pair"). This is essentially a pairwise alignment with score information. PsiBlastHSP objec...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits
This object implements a parser for BLASTN hit output....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a Bio::Search::ResultI in Text.
This object implements the SearchWriterI interface which will produce a set of Text for a specific Bio::Search::Report::ReportI interface. You can also provide the argument -filters => \%hash to filter the at the hsp, hit, or result level. %hash is a...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC