Bio::DB::DBD - DESCRIPTION of Interface ++

Describe the interface here...

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

Deobfuscator - get BioPerl method and package information from a Berkeley DB 11 ++

The Deobfuscator module contains functions which relate to retrieving specific types of documentation about BioPerl packages and methods. The deob_index.pl script reads through all of the BioPerl files, extracts the documentation, and stores it in tw...

CJFIELDS/BioPerl-1.6.924 - 10 Jul 2014 20:22:23 GMT - Search in distribution

AlignAid - easily run sequence alignments locally or on a cluster ++

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...

DMESSINA/AlignAid-v0.0.2 - 16 Dec 2006 01:04:35 GMT - Search in distribution

Bio::Biblio - a bibliographic query service module 3 ++

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 ...

CDRAUG/Bio-Biblio-1.70 - 24 Mar 2013 00:19:52 GMT - Search in distribution

bp_einfo.pl - query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases) 1 ++

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...

CJFIELDS/Bio-EUtilities-1.73 - 09 Sep 2013 03:19:54 GMT - Search in distribution

data2bed.pl - A script to convert a data file to a bed file. ++

This program will convert a tab-delimited data file into a BED file, according to the specifications here <http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED>. A minimum of three and a maximum of six columns may be generated. Thin and thick ...

TJPARNELL/Bio-ToolBox-1.25 - 13 Mar 2015 03:28:57 GMT - Search in distribution

Bio::DB::Sam - Read SAM/BAM database files 3 ++

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-1.41   (1 review) - 22 Dec 2014 21:45:13 GMT - Search in distribution

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-1.006900 - 21 Apr 2011 16:23:41 GMT - Search in distribution

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 format can be found a...

TJPARNELL/Bio-DB-USeq-0.22 - 27 Apr 2014 03:41:56 GMT - Search in distribution

Bio::Graphics - Generate GD images of Bio::Seq objects ++

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

LDS/Bio-Graphics-2.39 - 31 Jul 2014 02:32:25 GMT - Search in distribution

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

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...

CJFIELDS/Bundle-BioPerl-2.1.9 - 16 Jan 2015 20:05:40 GMT - Search in distribution

GO::AppHandle - Gene Ontology Data API handle ++

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...

SJCARBON/go-db-perl-0.04 - 21 Dec 2009 21:56:44 GMT - Search in distribution

GOBO::Doc::FAQ - Frequently Asked Questions ++
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 GMT - Search in distribution

FAST::Bio::Seq - Sequence object, with features ++

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-1.05 - 14 Apr 2015 07:14:22 GMT - Search in distribution

load_genbank.pl - Load a Bio::DB::GFF database from GENBANK files. ++

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-2.55 - 10 Jul 2013 14:51:25 GMT - Search in distribution

Bio::SABio::NCBI - Downloads and parse DNA data from NCBI site ++

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   (1 review) - 11 Jun 2002 17:10:21 GMT - Search in distribution

Fry::Lib::BioPerl - Commandline enables common tasks for sequence and alignment objects for Bio::Perl modules. ++

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 GMT - Search in distribution

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

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 GMT - Search in distribution

Bio::DB::NextProt - Object interface to neXtProt REST API. ++

The module allows the dynamic retrieval of information from the neXtProt Database through its API service. All the information below was extracted from the API webpage. For the moment the results obtained from the API are in pure HTML, XML or JSON. S...

LEPREVOST/Bio-DB-NextProt-1.05 - 18 Oct 2014 19:21:50 GMT - Search in distribution

Bio::Community::IO - Read and write files that describe communities ++

A Bio::Community::IO object implement methods to read and write communities in formats used by popular programs such as BIOM, GAAS, QIIME, Unifrac, or as generic tab-separated tables. The format should be automatically detected though it can be manua...

FANGLY/Bio-Community-0.001007 - 28 May 2014 06:28:28 GMT - Search in distribution