Abstract
Summary Microbial functional diversification is driven by environmental factors. In some cases, microbes differ more across environments than across taxa. We have recently developed fusion+, a network-based method for comparing microbial functionality on the basis of whole proteome sequences. Here we introduce fusionDB, a novel database of microbial functional similarities, indexed by available environmental preferences. fusionDB entries represent nearly fourteen hundred taxonomically-distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Any given database search produces an easily visualizable XML-formatted network file of selected organisms, displaying functions shared by the selected organisms. fusionDB thus provides a fast means of associating specific environmental factors with organism functions.
Availability http://bromberglab.org/databases/fusiondb and as a sql-dump by request.
Contact czhu{at}bromberglab.org, ymahlich{at}bromberglab.org
Supplementary information Supplementary data are available at Bioinformatics online