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

Allows the dynamic retrieval of Bio::Seq sequence objects from the GenBank 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. Note that when quer...

CJFIELDS/Bio-DB-NCBIHelper-1.7.7 - 30 Jun 2021 13:56:04 UTC - Search in distribution

Bio::DB::Flat::BDB::genbank - genbank adaptor for Open-bio standard BDB-indexed flat file River stage two • 60 direct dependents • 65 total dependents

This module allows genbank files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use it via Bio::DB::Flat....

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution

load_genbank.pl - Load a Bio::DB::GFF database from GENBANK files. River stage zero No dependents

This script loads a Bio::DB::GFF database with the features contained in a either a local genbank file or an accession that is fetched from genbank. Various command-line options allow you to control which database to load and whether to allow an exis...

LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC - Search in distribution

Bio::Graphics - Generate GD images of Bio::Seq objects River stage one • 2 direct dependents • 2 total dependents

Please see Bio::Graphics::Panel for the full interface. Also try the script glyph_help.pl for quick help on glyphs and their options....

CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC - Search in distribution

Boulder::Genbank - Fetch Genbank data records as parsed Boulder Stones River stage zero No dependents

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...

LDS/Boulder-1.30 - 14 Dec 2002 02:06:29 UTC - Search in distribution

Bio::Das - Interface to Distributed Annotation System River stage zero No dependents

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:...

LDS/Bio-Das-1.17 - 29 Jun 2010 19:43:55 UTC - Search in distribution

bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files. River stage one • 2 direct dependents • 2 total dependents

This script loads a Bio::DB::GFF database with the features contained in a either a local genbank file or an accession that is fetched from genbank. Various command-line options allow you to control which database to load and whether to allow an exis...

CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC - Search in distribution

load_seqdatabase.pl River stage zero No dependents

This script loads a BioSQL database with sequences. There are a number of options that have to do with where the database is and how it's accessed and the format and namespace of the input files. These are followed by any number of file names. The fi...

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

FAST::Bio::Seq - Sequence object, with features River stage zero No dependents

A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently FAST::Bio...

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - 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 UTC - Search in distribution

Bio::Network::ProteinNet - a representation of a protein interaction graph. River stage zero No dependents

A ProteinNet is a representation of a protein interaction network. Its functionality comes from the Graph module of Perl and from BioPerl, the nodes or vertices in the network are Sequence objects. Nodes A node is one or more BioPerl sequence objects...

CJFIELDS/BioPerl-Network-1.006902 - 07 Nov 2011 16:27:40 UTC - 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 UTC - Search in distribution

Bio::BLAST::Database - work with formatted BLAST databases River stage one • 1 direct dependent • 1 total dependent

Each object of this class represents an NCBI-formatted sequence database on disk, which is a set of files, the exact structure of which varies a bit with the type and size of the sequence set. This is mostly an object-oriented wrapper for using NCBI'...

RBUELS/Bio-BLAST-0.4 - 12 Sep 2011 15:47:19 UTC - 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 UTC - Search in distribution

Fry::Lib::BioPerl - Commandline enables common tasks for sequence and alignment objects for Bio::Perl modules. River stage zero No dependents

The main point of this library is to view,retrieve and create sequences and alignments. All objects created are indexed by the shell as Fry::Obj objects. See Fry::Lib::Default for commands that you can perform on these objects. Sequence and alignment...

BOZO/Fry-Lib-BioPerl-0.15 - 14 Jan 2005 20:54:17 UTC - Search in distribution

Bio::DB::SoapEUtilities - Interface to the NCBI Entrez web service *BETA* River stage one • 2 direct dependents • 2 total dependents

This module allows the user to query the NCBI Entrez database via its SOAP (Simple Object Access Protocol) web service (described at <http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.h tml>). The basic tools ("einfo, esearch, eli...

CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution

Bio::LITE::Taxonomy::NCBI - Lightweight and efficient NCBI taxonomic manager River stage two • 1 direct dependent • 10 total dependents

This module provides easy and efficient access to the NCBI taxonomy with minimal dependencies and without intermediary databases. This module is not part of the Bioperl bundle. For bioperl alternatives see the "SEE ALSO" section of this document....

MOTIF/Bio-LITE-Taxonomy-NCBI-0.1 - 20 May 2015 08:51:23 UTC - Search in distribution

Bio::DB::SeqFeature::Store::FeatureFileLoader - feature file loader for Bio::DB::SeqFeature::Store River stage zero No dependents

The Bio::DB::SeqFeature::Store::FeatureFileLoader object parsers FeatureFile-format sequence annotation files and loads Bio::DB::SeqFeature::Store databases. For certain combinations of SeqFeature classes and SeqFeature::Store databases it features a...

CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC - Search in distribution
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