The Bioinformatics Databank Manager System.
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
conf
doc
docker
external/bin
jar
scripts
src
tests/junit
.gitignore
.travis.yml
LICENSE.txt
NOTICE.txt
README.md
TODOs.txt
build.xml

README.md

BeeDeeM: the Bioinformatics Databank Manager System

License AGPL Build Status

BeeDeeM is a general purpose Bioinformatics Databank Manager.

It provides a suite of command-line and UI softwares to install and use major sequence databanks and biological classifications. It is the ideal companion of the NCBI BLAST suite of softwares.

Main features

BeeDeeM automatically performs:

  • the download of the database files from remote sites (via FTP),
  • the decompression of the files (gzip files),
  • the un-archiving of the files (tar files),
  • the conversion of native sequence banks (e.g. Genbank) to FASTA files,
  • the preparation of databases in BLAST format from native sequence bank formats,
  • the indexing of Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl, Fasta, Silva and BOLD files allowing their efficient querying by way of sequence identifiers,
  • the indexing of sequence features and ontologies data (NCBI Taxonomy, Gene Ontology, Enzyme Commission and Intepro domains),
  • the preparation of taxonomic subsets out of annotated sequence banks,
  • the filtering of sequence banks with user-defined constraints.

More.

Main tools

BeeDeeM provides a toolchain made of:

  • a command-line tool to automate databanks installation
  • a UI front-end to do the same in a more friendly way (see below)
  • a command-line tool to annotate BLAST results
  • a command-line to query databanks using sequence IDs

More.

UiManager

Practical use cases

Among others, these databanks can be used to:

  • prepare and maintain up-to-date local copy of usefull data
  • run BLAST sequence comparison jobs
  • annotate BLAST results with sequence features and ontologies

Companion tools

BeeDeeM features and data are accessible from:

This manual explains how to install, configure and use BeeDeeM.

Requirements

Use a Java Virtual Machine 1.7 (or above) from Oracle.

Not tested with any other JVM providers but Oracle... so there is no guarantee that the software will work as expected if not using Oracle's JVM. More about BeeDeeM requirements.

Software installation, use and configuration

License and dependencies

BeeDeeM itself is released under the GNU Affero General Public License, Version 3.0. AGPL

It depends on several thrid-party libraries as stated in the NOTICE.txt file provided with this project.

-- (c) 2007-2017 - Patrick G. Durand and Ludovic Antin