The Bioinformatics Databank Manager System (BeeDeeM) is capable of installing on a local computing system major sequence databank file formats: Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl, Fasta, Silva and BOLD. In addition to sequence data files, BeeDeeM can install major biological classifications (ontologies), such as NCBI Taxonomy, Gene Ontology, Enzyme Commission and Intepro domains.
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 (screenshot, below)
- a command-line tool to annotate BLAST results
- a command-line to query databanks using sequence IDs
Among others, these databanks can be used to:
- prepare and maintain up-to-date local copy of useful data
- run BLAST sequence comparison jobs
- annotate BLAST results with sequence features and ontologies
You can review all the features of the software by having a look at its user manual.
BeeDeeM is running on Linux, MacOSX and Windows. Major requirements of the software: a Java Runtime 1.7+, a 64bits computer and potentially a huge amount of disk space (depending on which banks you install). BeeDeeM comes with NCBI's makeblastdb to prepare BLAST banks; however, BeeDeeM does not comes with the entire BLAST suite of software.
BeeDeeM is a free open source software available on Github, here.