Bio::DB::HTS::Query - Object representing the query portion of a BAM/SAM alignment

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This is a simple Bio::SeqFeatureI object that represents the query part of a SAM alignment. Methods POD ERRORS Hey! The above document had some coding errors, which are explained below: Around line 8: =over is the last thing in the document?!...

• Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
• Bio::DB::HTS::VCF - Read VCF/BCF data files
• Bio::DB::HTS::Tabix - Object oriented access to the underlying tbx C methods
• 3 more results from Bio-DB-HTS »

Bio::DB::Bam::Query - Object representing the query portion of a BAM/SAM alignment

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This is a simple Bio::SeqFeatureI object that represents the query part of a SAM alignment. Methods POD ERRORS Hey! The above document had some coding errors, which are explained below: Around line 8: =over is the last thing in the document?!...

• Bio::DB::Sam - Read SAM/BAM database files
• Bio::DB::Bam::Alignment - The SAM/BAM alignment object
• Bio::DB::Bam::Target - Object representing the query portion of a BAM/SAM alignment in NATIVE alignment

Bio::DB::Query::GenBank - Build a GenBank Entrez Query

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This class encapsulates NCBI Entrez queries. It can be used to store a list of GI numbers, to translate an Entrez query expression into a list of GI numbers, or to count the number of terms that would be returned by a query. Once created, the query o...

• bp_query_entrez_taxa - query Entrez taxonomy database and print out information
• bp_download_query_genbank - script to query Genbank and retrieve records
• Bio::DB::GenPept - Database object interface to GenPept
• 4 more results from Bio-DB-NCBIHelper »

Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies

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Do not use this class directly. See Bio::DB::QueryI and one of the implementor classes (such as Bio::DB::Query::GenBank) for information. Those writing subclasses must define _get_params() and _parse_response(), and possibly override _request_method(...

• Bio::DB::QueryI - Object Interface to queryable sequence databases
• Bio::DasI - DAS-style access to a feature database
• Bio::Ontology::Term - implementation of the interface for ontology terms
• 10 more results from BioPerl »

Bio::DB::Query::SqlQuery - Object representing an SQL Query

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This class inherits from Bio::DB::Query::AbstractQuery...

• Bio::DB::Query::BioQuery - Object representing a query on a bioperldb
• Bio::DB::Query::SqlGenerator - Object representing an SQL Query
• Bio::DB::Query::QueryResultI - DESCRIPTION of Interface
• 26 more results from BioPerl-DB »

Bio::DB::SoapEUtilities::GQueryAdaptor - Handle for Entrez SOAP GlobalQuery items

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This adaptor provides an iterator ("next_query()") and other convenience functions for parsing NCBI Entrez EUtility "egquery" SOAP results....

• Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
• Bio::Tools::Run::StandAloneBlast - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.
• Bio::DB::SoapEUtilities::Result - Accessor object for SoapEUtilities results
• 6 more results from BioPerl-Run »

Bio::Biblio - a bibliographic query service module

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This is a class whose instances can access bibliographic repositories. It allows one to query a bibliographic database (such as MEDLINE) and then to retrieve resulting citations from it. The citations are returned in an XML format which is native to ...

• Bio::DB::BiblioI - an interface to a Bibliographic Query Service
• Bio::DB::Biblio::soap - a SOAP-based access to a bibliographic query service
• Bio::DB::Biblio::eutils - access to PubMed's bibliographic query service

AlignAid - easily run sequence alignments locally or on a cluster

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AlignAid is designed to make it easy to run the sequence alignment programs Blast and cross_match. AlignAid can accept a large number of query sequences. If a compute cluster queue such as LSF or PBS is available, AlignAid can automatically split the...

DBUtils - a module for useful Database utilities

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Helper functions for achieving common DB tasks with a GeneX DB....

• Bio::Genex::Sample - Methods for processing data from the GeneX DB table: Sample
• Bio::Genex::Sample - Methods for processing data from the GeneX DB table: Sample
• Bio::Genex::Contact - Methods for processing data from the GeneX DB table: Contact
• 65 more results from Bio-Genex »

GO::AppHandle - Gene Ontology Data API handle

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This is a module for accessing Gene Ontology data sources, e.g the GO relational database. It defines a set of methods that provide a consistent interface independent of the way the GO data is stored. For an explanation of the GO project, please visi...

MCE::Shared - MCE extension for sharing data supporting threads and processes

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This module provides data sharing capabilities for MCE supporting threads and processes. MCE::Hobo provides threads-like parallelization for running code asynchronously....

get_datasets.pl - A program to collect data for a list of features

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This program will collect dataset values from a variety of sources, including features in a BioPerl Bio::DB::SeqFeature::Store database, binary wig files .wib loaded in a database using Bio::Graphics::Wiggle, bigWig files, bigBed files, Bam alignment...

• get_binned_data.pl - A program to collect data in bins across a list of features.
• get_relative_data.pl - A program to collect data in bins around a relative position.

pod::INSTALL

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• pod::CONFIGURE_HOWTO
• Bio::Graphics::Browser::Plugin - Base class for gbrowse plugins.
• Bio::Graphics::Browser2::Plugin - Base class for gbrowse plugins.
• 1 more result from GBrowse »

bp_einfo - Query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases).

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Command line options: -e/--email Valid email (required by NCBI policy) -d/--db/--database NCBI database to query (default = none, which shows available databases) -f/--field print out information about a specific field code (default = none) -l/--link...

• Bio::EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils
• Bio::DB::EUtilities - Webagent which interacts with and retrieves data from NCBI's eUtils.
• Bio::Tools::EUtilities - NCBI eutil XML parsers.
• 4 more results from Bio-EUtilities »

Bio::Das - Interface to Distributed Annotation System

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Bio::Das provides access to genome sequencing and annotation databases that export their data in Distributed Annotation System (DAS) format version 1.5. This system is described at http://biodas.org. Both unencrypted (http:) and SSL-encrypted (https:...

• Bio::Das::Segment - Serial access to Bio::Das sequence "segments"

Data::Type - robust and extensible data- and valuetype system

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A lot of CPAN modules have a common purpose: reporting if data has some "characteristics". Email::Valid is an illustrous example: reporting if a string has characteristics of an email address. The "address()" method reports this via returning 'yes' o...

• Data::Type::Collection - a group of datatypes somehow related

Boulder::Genbank - Fetch Genbank data records as parsed Boulder Stones

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Boulder::Genbank provides retrieval and parsing services for NCBI Genbank-format records. It returns Genbank entries in Stone format, allowing easy access to the various fields and values. Boulder::Genbank is a descendent of Boulder::Stream, and prov...

Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl 1.5.2

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The BioPerl distribution from http://bioperl.org contains code and modules that may use or require additional 'external' perl modules for advanced functionality. Many of the external modules are not contained within the standard Perl distribution. Th...

TAIR::Blast - A module to gather automated BLAST result from TAIR (http://www.arabidopsis.org/Blast/index.jsp)

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XML::EasySQL - a two-way SQL/XML base class for Perl. It was written by Curtis Lee Fulton (http://fultron.net; curtisf@fultron.net).

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XML::EasySQL is a two-way SQL/XML base class for Perl. It acts as an emulsifier for the oil and water that is SQL and XML. Features: o Two-way transforms between XML and SQL data o smart SQL updates: only altered tables are updated o unlimited tree d...