Search results for "Bio::DB"
Bio::DB::Ace - Database object interface to ACeDB servers
This provides a standard BioPerl database access to Ace, using Lincoln Steins excellent AcePerl module. You need to download and install the aceperl module from http://stein.cshl.org/AcePerl/ before this interface will work. This interface is designe...
CJFIELDS/Bio-DB-Ace-1.7.3 - 25 Sep 2018 00:11:27 UTC - Search in distribution- Bio::DB::GFF::Adaptor::ace - ace interface (for multiple inheritance)
- Bio::DB::GFF::Adaptor::dbi::mysqlace - Unholy union between mysql GFF database and acedb database
- Bio::DB::GFF::Adaptor::dbi::oracleace - Unholy union between oracle GFF database and acedb database
- 1 more result from Bio-DB-Ace »
Bio::DB::Big - Read files using bigWigLib including BigBED and BigWig
AYATES/Bio-DB-Big-v1.0.1
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16 Oct 2017 14:14:22 UTC
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- Bio::DB::Big - Interface to BigWig and BigBed files via libBigWig
- Bio::DB::Big::File - Object representing a UCSC big file
- Bio::DB::Big::AutoSQL
- 1 more result from Bio-DB-Big »
Bio::DB::GFF - Storage and retrieval of sequence annotation data
Bio::DB::GFF provides fast indexed access to a sequence annotation database. It supports multiple database types (ACeDB, relational), and multiple schemas through a system of adaptors and aggregators. The following operations are supported by this mo...
CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC - Search in distribution- Bio::DB::GFF::Homol - A segment of DNA that is homologous to another
- Bio::DB::GFF::Segment - Simple DNA segment object
- Bio::DB::GFF::Feature - A relative segment identified by a feature type
- 45 more results from Bio-DB-GFF »
Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
This module provides a Perl interface to the HTSlib library for indexed and unindexed SAM/BAM/CRAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information a...
AVULLO/Bio-DB-HTS-3.01 - 23 Apr 2019 13:51:11 UTC - Search in distribution- Bio::DB::HTS::VCF - Read VCF/BCF data files
- Bio::DB::HTS::Kseq - Bindings to Kseq
- Bio::DB::HTS::Faidx - Perl extension for accessing bgzip compressed and indexed FASTA using htslib
- 19 more results from Bio-DB-HTS »
Bio::DB::Sam - Read SAM/BAM database files
This module provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC - Search in distribution- Bio::DB::Bam::Query - Object representing the query portion of a BAM/SAM alignment
- Bio::DB::Bam::Pileup - Object passed to pileup() callback
- Bio::DB::Bam::Target - Object representing the query portion of a BAM/SAM alignment in NATIVE alignment
- 8 more results from Bio-SamTools »
Bio::DB::DBD - DESCRIPTION of Interface
Describe the interface here...
CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 UTC - Search in distribution- Bio::DB::DBI - DESCRIPTION of Interface
- Bio::DB::BioDB - class creating the adaptor factory for a particular database
- Bio::DB::DBI::Pg - DESCRIPTION of Object
- 72 more results from BioPerl-DB »
Bio::DB::EMBL - Database object interface for EMBL entry retrieval
Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL database using the dbfetch script at EBI: <http://www.ebi.ac.uk/Tools/dbfetch/dbfetch>. In order to make changes transparent we have host type (currently only ebi) and location (...
CJFIELDS/Bio-DB-EMBL-1.7.4 - 04 Mar 2019 05:02:40 UTC - Search in distribution
Bio::DB::TFBS - Access to a Transcription Factor Binding Site database
This is a front end module for access to a Transcription Factor Binding Site database....
CJFIELDS/Bio-DB-TFBS-1.7.3 - 25 Sep 2018 00:20:12 UTC - Search in distribution- Bio::DB::TFBS::transfac_pro - An implementation of Bio::DB::TFBS which uses local flat files for transfac pro
Bio::DB::USeq - Read USeq archive database files
Bio::DB::USeq is a BioPerl style adaptor for reading USeq files. USeq files are compressed, indexed data files supporting modern bioinformatic datasets, including genomic points, scores, and intervals. More information about the USeq software package...
TJPARNELL/Bio-DB-USeq-0.26 - 24 Sep 2022 02:31:45 UTC - Search in distribution- USeqInfo.pl - A script to collect basic information about a USeq archive.
Bio::DB::SeqI - Abstract Interface for Sequence databases
Abstract interface for a sequence database...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::DB::Qual - Fast indexed access to quality files
- Bio::DB::Flat - Interface for indexed flat files
- Bio::DB::Fasta - Fast indexed access to fasta files
- 72 more results from BioPerl »
Bio::DB::ESoap - Client for the NCBI Entrez EUtilities SOAP server
"ESoap" provides a basic SOAP interface to the NCBI Entrez Utilities Web Service (<http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help. html>). SOAP::Lite handles the SOAP calls. Higher level access, pipelines, BioPerl object I/O an...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution- Bio::DB::ESoap::WSDL - WSDL parsing for Entrez SOAP EUtilities
- Bio::DB::SoapEUtilities - Interface to the NCBI Entrez web service *BETA*
- Bio::DB::SoapEUtilities::Result - Accessor object for SoapEUtilities results
- 16 more results from BioPerl-Run »
Bio::DB::RefSeq - Database object interface for RefSeq retrieval
Allows the dynamic retrieval of sequence objects Bio::Seq from the RefSeq nucleotide database using the dbfetch script at EBI: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch At this time the module specifically retrieves nucleotide sequences only. In ord...
CJFIELDS/Bio-DB-RefSeq-1.7.4 - 07 Dec 2019 22:10:26 UTC - Search in distribution
Bio::DB::Tagger - Simple object tagging system
This is a simple object tagger interface that provides relational support for tagging objects (identified by string IDs) with arbitrary string tags. METHODS $tagger = Bio::DB::Tagger->new(@args) Constructor for the tagger class. Arguments are: -dsn <...
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC - Search in distribution- Bio::DB::Tagger::Tag - Authored tags
- Bio::DB::GFF::Aggregator::match_gap - GFF3 match aggregator
- Bio::DB::SeqFeature::Store::LoadHelper - Internal utility for Bio::DB::SeqFeature::Store
- 37 more results from GBrowse »
Bio::DB::BiblioI - an interface to a Bibliographic Query Service
This interface describes the methods for accessing a bibliographic repository, for querying it and for retrieving citations from it. The retrieved citations are in XML format and can be converted to perl objects using *Bio::Biblio::IO*. The interface...
CDRAUG/Bio-Biblio-1.70 - 24 Mar 2013 00:19:52 UTC - Search in distribution- Bio::DB::Biblio::soap - a SOAP-based access to a bibliographic query service
- Bio::DB::Biblio::eutils - access to PubMed's bibliographic query service
- Bio::DB::Biblio::biofetch - a BioFetch-based access to a bibliographic citation retrieval
- 1 more result from Bio-Biblio »
Bio::DB::BigFile - Low-level interface to BigWig & BigBed files
This module provides a low-level interface to Jim Kent's BigWig and BigBed files, which are indexed genome feature databases that can be randomly accessed across the network. Please see http://genome.ucsc.edu/FAQ/FAQformat.html for information about ...
LDS/Bio-BigFile-1.07 - 24 Feb 2012 17:20:46 UTC - Search in distribution
Bio::DB::GenPept - Database object interface to GenPept
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept database at NCBI, via an Entrez query. WARNING: Please do NOT spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. Batch Entrez supp...
CJFIELDS/Bio-DB-NCBIHelper-1.7.8 - 15 Dec 2023 04:25:18 UTC - Search in distribution- Bio::DB::GenBank - Database object interface to GenBank
- Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases.
- Bio::DB::EntrezGene - Database object interface to Entrez Gene
- 5 more results from Bio-DB-NCBIHelper »
Bio::BioStudio::DB
BioStudio functions for database interaction....
NOTDOCTOR/Bio-BioStudio-2.11 - 04 Dec 2015 18:59:24 UTC - Search in distribution
Bio::DB::SwissProt - Database object interface to SwissProt retrieval
SwissProt is a curated database of proteins managed by the Swiss Bioinformatics Institute. Additional tools for parsing and manipulating swissprot files can be found at ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/. Allows the dynamic retrie...
CJFIELDS/Bio-DB-SwissProt-1.7.4 - 07 Dec 2019 22:09:00 UTC - Search in distribution
Bio::DB::Das::Chado - DAS-style access to a chado database
Bio::DB::Das::Chado allows DAS style access to a Chado database, getting SeqFeatureI-compliant BioPerl objects and allowing GBrowse to access a Chado database directly....
SCAIN/Bio-DB-Das-Chado-0.35a - 07 Apr 2015 23:02:17 UTC - Search in distribution- Bio::DB::Das::Chado::Segment - DAS-style access to a chado database
- Bio::DB::Das::Chado::Segment::Feature
- gmod_chado_fts_prep.pl - prepares a Chado schema to use full text searching
Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store
The Bio::DB::SeqFeature object is the default SeqFeature class stored in Bio::DB::SeqFeature databases. It implements both the Bio::DB::SeqFeature::NormalizedFeatureI and Bio::DB::SeqFeature::NormalizedTableFeatureI interfaces, which means that its s...
CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC - Search in distribution- Bio::DB::SeqFeature::Store - Storage and retrieval of sequence annotation data
- Bio::DB::SeqFeature::Segment - Location-based access to genome annotation data
- Bio::DB::SeqFeature::NormalizedFeature - Normalized feature for use with Bio::DB::SeqFeature::Store
- 16 more results from Bio-DB-SeqFeature »