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Nucleic Acids Research Advance Access originally published online on October 14, 2008
Nucleic Acids Research 2009 37(Database issue):D494-D498; doi:10.1093/nar/gkn674
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Nucleic Acids Research, 2009, Vol. 37, Database issue D494-D498
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform ‘Open Genome Resource’ (OGeR)

Johannes Klein, Richard Münch, Ilona Biegler, Isam Haddad, Ida Retter* and Dieter Jahn

Institute for Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany

*To whom correspondence should be addressed. Tel: +49 531 391 5810; Fax: +49 531 391 5854; Email: i.retter{at}tu-bs.de

Received August 15, 2008. Revised September 19, 2008. Accepted September 22, 2008.

Streptococci are the causative agent of many human infectious diseases including bacterial pneumonia and meningitis. Here, we present Strepto-DB, a database for the comparative genome analysis of group A (GAS) and group B (GBS) streptococci. The known genomes of various GAS and GBS contain a large fraction of distributed genes that were found absent in other strains or serotypes of the same species. Strepto-DB identifies the homologous proteins deduced from the genomes of interest. It allows for the elucidation of the GAS and GBS core- and pan-genomes via genome-wide comparisons. Moreover, an intergenic region analysis tool provides alignments and predictions for transcription factor binding sites in the non-coding sequences. An interactive genome browser visualizes functional annotations. Strepto-DB (http://oger.tu-bs.de/strepto_db) was created by the use of OGeR, the Open Genome Resource for comparative analysis of prokaryotic genomes. OGeR is a newly developed open source database and tool platform for the web-based storage, distribution, visualization and comparison of prokaryotic genome data. The system automatically creates the dedicated relational database and web interface and imports an arbitrary number of genomes derived from standardized genome files. OGeR can be downloaded at http://oger.tu-bs.de.


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