title: VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria.
abstract: 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. VRprofile is freely available at http://bioinfo-mml.sjtu.edu.cn/VRprofile.
authors.affiliation: College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Cui
authors.initials: C
authors.lastname: Tai
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Zixin
authors.initials: Z
authors.lastname: Deng
authors.affiliation: College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China.
authors.forename: Weihong
authors.initials: W
authors.lastname: Zhong
authors.affiliation: Department of microbiology and immunology research, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Yongqun
authors.initials: Y
authors.lastname: He
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Hong-Yu
authors.initials: HY
authors.lastname: Ou
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D002874:Chromosome Mapping; D004352:Drug Resistance, Microbial; D020869:Gene Expression Profiling; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D005810:Multigene Family; D012984:Software; D014774:Virulence