Bio::DB::Ace - Database object interface to ACeDB servers River stage zero No dependents

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 GMT - Search in distribution

Bio::DB::Big - Read files using bigWigLib including BigBED and BigWig River stage one • 1 direct dependent • 1 total dependent

AYATES/Bio-DB-Big-v1.0.1 - 16 Oct 2017 14:14:22 GMT - Search in distribution

Bio::DB::GFF - Storage and retrieval of sequence annotation data River stage one • 2 direct dependents • 2 total dependents

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 GMT - Search in distribution

Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files River stage one • 1 direct dependent • 1 total dependent

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 GMT - Search in distribution

Bio::DB::Sam - Read SAM/BAM database files River stage one • 2 direct dependents • 2 total dependents

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 GMT - Search in distribution

Bio::DB::DBD - DESCRIPTION of Interface River stage zero No dependents

Describe the interface here...

CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 GMT - Search in distribution

Bio::DB::EMBL - Database object interface for EMBL entry retrieval River stage one • 1 direct dependent • 8 total dependents

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 GMT - Search in distribution

Bio::DB::TFBS - Access to a Transcription Factor Binding Site database River stage zero No dependents

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 GMT - Search in distribution

Bio::DB::USeq - Read USeq archive database files River stage zero No dependents

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-0.25 - 02 Jan 2019 19:51:06 GMT - Search in distribution
  • USeqInfo.pl - A script to collect basic information about a USeq archive.

Bio::DB::Flat - Interface for indexed flat files River stage two • 74 direct dependents • 79 total dependents

This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see Bio::Index::Abstract), this is specialized to work with the "flat index" and BerkeleyDB indexed flat fil...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 GMT - Search in distribution

Bio::DB::ESoap - Client for the NCBI Entrez EUtilities SOAP server River stage one • 6 direct dependents • 7 total dependents

"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 GMT - Search in distribution

Bio::DB::RefSeq - Database object interface for RefSeq retrieval River stage one • 1 direct dependent • 8 total dependents

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 GMT - Search in distribution

Bio::DB::Tagger - Simple object tagging system River stage zero No dependents

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 GMT - Search in distribution

Bio::DB::BiblioI - an interface to a Bibliographic Query Service River stage zero No dependents

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 GMT - Search in distribution

Bio::DB::BigFile - Low-level interface to BigWig & BigBed files River stage one • 1 direct dependent • 1 total dependent

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 GMT - Search in distribution

Bio::DB::GenPept - Database object interface to GenPept River stage two • 3 direct dependents • 10 total dependents

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-1.7.6 - 07 Dec 2019 22:14:42 GMT - Search in distribution

Bio::BioStudio::DB River stage zero No dependents

BioStudio functions for database interaction....

NOTDOCTOR/Bio-BioStudio-2.11 - 04 Dec 2015 18:59:24 GMT - Search in distribution

Bio::DB::SwissProt - Database object interface to SwissProt retrieval River stage one • 1 direct dependent • 8 total dependents

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 GMT - Search in distribution

Bio::DB::Das::Chado - DAS-style access to a chado database River stage zero No dependents

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 GMT - Search in distribution

Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store River stage zero No dependents

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 GMT - Search in distribution

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