Abstract: Systems biology approaches to bacteria require an integrated
database and a bioinformatics tool platform to enable automated and manual
annotation, regulatory and metabolic network deduction, and the storage of
related experimental as well as predicted data. In this context ROSY – the
Roseobacter SYstems biology database – was developed for completed and
draft genomes of representatives of the marine Roseobacter clade, which
constitutes one of the most abundant bacterial clades in the ocean. ROSY
provides an integrative view on comprehensive data collections such as KEGG,
GenBank, RoseoBase, BRENDA, and PRODORIC as well as mediates the use of
connected tools for promoter analysis (Virtual Footprint), genome and pathway
visualization (CGView, PathCompare), and prediction of signal peptides
(PrediSi). Moreover, metabolome, transcriptome, and proteome data can be stored
in ROSY, supplying an integrated platform for comparative genomics and systems
biology. This entire database system along with the data retrieval, comparative
analysis, and website presentation tools (http://rosy.tu-bs.de) can be easily
adopted for the systems biological analysis of other bacterial groups.
