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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 and PLAST.

Main features

BeeDeeM automatically performs:

  • the download of the database files from remote sites (via FTP, Aspera),
  • 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 and Fasta files allowing their efficient querying by way of sequence identifiers,
  • the indexing of sequence features and ontologies data (NCBI Taxonomy, Gene Ontology, Enzyme Commission, Intepro domains and PFAM 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.

Use BeeDeeM from the command line

Here is an example of a script to start Genbank_CoreNucleotide installation on Ifremer's DATARMOR supercomputer:

#!/usr/bin/env bash
#PBS -q web
#PBS -l mem=4gb
#PBS -l ncpus=8
#PBS -l walltime=72:00:00

# Release of BeeDeeM to use
BDM_HOME="$SOFT/bioinfo/beedeem"
BDM_VER="5.5.1"

# Load BeeDeeM environment
module load java/1.8.0_121

# prefix of '.dsc' file that must exist in $BDM_HOME/conf/descriptor
DESCRIPTOR="Genbank_CoreNucleotide"
export KL_LOG_FILE=${DESCRIPTOR}.log
$BDM_HOME/$BDM_VER/install.sh \
   -desc ${DESCRIPTOR} \
   >& "$HOME/beedeem/logs/${DESCRIPTOR}-pbs.out"

You can easily automate bank installation using such BeeDeeM based scripts with Unix cron scheduler.

Use BeeDeeM UI

Here is a screenshot of BeeDeeM user friendly interface:

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 1.8 (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) 2007-2020 - Patrick G. Durand and Ludovic Antin