RT Journal Article
SR Electronic
T1 <em>fusion</em>DB: assessing microbial diversity and environmental preferences via functional similarity networks
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 035923
DO 10.1101/035923
A1 C Zhu
A1 Y Mahlich
A1 Y Bromberg
YR 2016
UL http://biorxiv.org/content/early/2016/01/07/035923.abstract
AB 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@bromberglab.org, ymahlich@bromberglab.org