BeeDeeM: the Bioinformatics Databank Manager System
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.
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.
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
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
BeeDeeM features and data are accessible from:
This manual explains how to install, configure and use BeeDeeM.
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