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 UTC - 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 UTC - Search in distribution
  • USeqInfo.pl - A script to collect basic information about a USeq archive.

Bio::Util::AA - Basic Amino Acid utilities River stage one • 1 direct dependent • 1 total dependent

Provides a set of functions and predefined variables which are handy when working with Amino Acids....

KGALINSKY/Bio-Util-AA-v0.1.6 - 23 Jun 2011 19:52:18 UTC - Search in distribution

Bio::Das::Lite - Perl extension for the DAS (HTTP+XML) Protocol (http://biodas.org/) River stage zero No dependents

This module is an implementation of a client for the DAS protocol (XML over HTTP primarily for biological-data)....

RPETTETT/Bio-Das-Lite-2.11 - 06 May 2011 10:25:32 UTC - Search in distribution

Bio::Util::DNA - Basic DNA utilities River stage one • 1 direct dependent • 1 total dependent

Provides a set of functions and predefined variables which are handy when working with DNA....

KGALINSKY/Bio-Util-DNA-v0.2.1 - 23 Jun 2011 19:53:46 UTC - 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 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::RefSeq - Database object interface for RefSeq retrieval River stage one • 1 direct dependent • 9 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::DOOP::DOOP - DOOP API main module River stage zero No dependents

DoOP is a database containing orthologous clusters of promoters from Homo sapiens, Arabidopsis thaliana and other organisms. Visit the doop.abc.hu or doopsearch.abc.hu sites for more information or read the following article. Endre Barta, Endre Sebes...

RAZZOR/Bio-DOOP-DOOP-1.04 - 17 Aug 2009 12:59:38 UTC - Search in distribution

Bio::MUST::Core - Core classes and utilities for Bio::MUST River stage one • 7 direct dependents • 7 total dependents

This distribution is the base of the "Bio::MUST" module collection designed for writing phylogenomic applications in Perl. Their main strength lies in their transparent handling of the NCBI Taxonomy database (see <https://www.ncbi.nlm.nih.gov/taxonom...

DBAURAIN/Bio-MUST-Core-0.202310 - 18 Aug 2020 11:04:48 UTC - Search in distribution

Bio::Tools::Gel - Calculates relative electrophoretic migration distances River stage zero No dependents

This takes a set of sequences or Bio::Seq objects, and calculates their respective migration distances using: distance = dilation * (4 - log10(length(dna)); Source: Molecular Cloning, a Laboratory Manual. Sambrook, Fritsch, Maniatis. CSHL Press, 1989...

CJFIELDS/Bio-Tools-Gel-1.7.3 - 25 Sep 2018 01:48:58 UTC - 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 UTC - 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 UTC - Search in distribution

Bio::DB::GenPept - Database object interface to GenPept River stage two • 3 direct dependents • 11 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 UTC - Search in distribution

Bio::Genex::Fkey - Perl extension for representing Database Foreign Keys River stage zero No dependents

This is a utility class for storing information about foreign keys in the GeneX DB....

JASONS/Bio-Genex-2.6.0 - 06 Feb 2001 23:15:15 UTC - Search in distribution

Bio::MLST::Types - Moose types to use for validation. River stage zero No dependents

AJPAGE/Bio-MLST-Check-2.1.1706216 - 03 Mar 2017 16:23:59 UTC - Search in distribution

Bio::Trace::ABIF - Perl extension for reading and parsing ABIF (Applied Biosystems, Inc. Format) files River stage one • 1 direct dependent • 1 total dependent

VITA/Bio-Trace-ABIF-1.06 - 02 Nov 2016 11:16:32 UTC - Search in distribution

Bio::Network::IO - Class for reading and writing biological network data. River stage zero No dependents

This class is analagous to the SeqIO and AlignIO classes. To read in a file of a particular format, file and format are given as key/value pairs as arguments. The Bio::Network::IO checks that the appropriate module is available and loads it. At prese...

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

Bio::SABio::NCBI - Downloads and parse DNA data from NCBI site River stage zero No dependents

This module works also under Win32 ,it does not require any ather packeges,is much simplier for use and instalation.(after it will be released) .It will *not* force user to learn complicated object relations and behavior ,as the bioperl project,in ca...

TSIRKIN/NCBI-0.10 - 11 Jun 2002 17:10:21 UTC - Search in distribution

Bio::Index::Hmmer - indexes HMMER reports and supports retreival based on query River stage zero No dependents

This object allows one to build an index on a HMMER file (or files) and provide quick access to the HMMER report for that accession. For best results 'use strict'. You can also set or customize the unique key used to retrieve by writing your own func...

CJFIELDS/Bio-SearchIO-hmmer-1.7.3 - 25 Sep 2018 00:26:52 UTC - Search in distribution

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