Jan 6, 2016

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks

BioRxiv : the Preprint Server for Biology
Chengsheng ZhuYana Bromberg

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@bromberglab.org, ymahlich@bromberglab.org Supplementary information: Supplementary data are available at Bioinformatics online

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Mentioned in this Paper

Microorganism
Genome
Environment
Bio-Informatics
Gene Transfer, Horizontal
Proteome
Organism
Microbial
Exogenous Factors
Membrane Fusion

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