Tool: BeeDeeM: the bioinformatics databank manager system
3
gravatar for patrick.durand
2.8 years ago by
France
patrick.durand120 wrote:

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

enter image description here

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.

ADD COMMENTlink modified 2.7 years ago • written 2.8 years ago by patrick.durand120

Dear Patrick, Hi

Thank you for sharing this tool.

~ Best

ADD REPLYlink written 2.8 years ago by Farbod3.3k
0
gravatar for patrick.durand
2.7 years ago by
France
patrick.durand120 wrote:

A Docker support has been added to facilitate the use of BeeDeeM. Read this.

ADD COMMENTlink written 2.7 years ago by patrick.durand120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 657 users visited in the last hour