Journal
BRIEFINGS IN BIOINFORMATICS
Volume 19, Issue 4, Pages 566-574Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbw141
Keywords
bacterial genome analysis; gene cluster searches; type III/IV/VI secretion system; mobile genetic element; genomic island prediction
Funding
- 973 program from the Ministry of Science and Technology, China [2015CB554202]
- National Natural Science Foundation of China [31670074, 31371261, 31670115]
- Specialized Research Fund for the Doctoral Program of Higher Education, China [20130073110062]
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VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands. VRprofile is thus able to co-localize the homologs of these conserved gene clusters using HMMer or BLASTp searches. With the integration of the homologous gene cluster search module with a sequence composition module, VRprofile has exhibited better performance for island-like region predictions than the other widely used methods. In addition, VRprofile also provides an integrated Web interface for aligning and visualizing identified gene clusters with MobilomeDB-archived gene clusters, or a variety set of bacterial genomes. VRprofile might contribute to meet the increasing demands of re-annotations of bacterial variable regions, and aid in the real-time definitions of disease-relevant gene clusters in pathogenic bacteria of interest.
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