MicrobeDB: a locally maintainable database of microbial genomic sequences

Bioinformatics. 2012 Jul 15;28(14):1947-8. doi: 10.1093/bioinformatics/bts273. Epub 2012 May 9.

Abstract

Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction with the database through an easy to use programming interface. MicrobeDB creates a simple to use, easy to maintain, centralized local resource for various large-scale comparative genomic analyses and a back-end for future microbial application design.

Availability: MicrobeDB is freely available under the GNU-GPL at: http://github.com/mlangill/microbedb/

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • Databases, Genetic*
  • Genome, Archaeal*
  • Genome, Bacterial*
  • Genomics
  • Internet
  • Software
  • User-Computer Interface