Paper Info
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.
Year
DOI
Venue
2018
10.1093/bib/bbw141
BRIEFINGS IN BIOINFORMATICS
Keywords
Field
DocType
bacterial genome analysis,gene cluster searches,type III/IV/VI secretion system,mobile genetic element,genomic island prediction
Gene cluster,Genome,Antibiotic resistance,Pathogenic bacteria,Biology,Genetics,Virulence
Journal
Volume
Issue
ISSN
19
4
1467-5463
Citations 
PageRank 
References 
4
0.49
28
Authors
6
Name
Order
Citations
PageRank
Jun Li140.82
Cui Tai2304.19
Zixin Deng3395.74
Weihong Zhong440.49
Yongqun He553.54
Hong-Yu Ou6324.05