摘要

VRprofile是一个Web服务器，可以帮助快速调查毒力和抗生素抗性基因，并在新测序的致病细菌基因组中扩展这些性状转移相关的遗传背景。使用的后端数据库MobilomeDB首先建立在已知的III / IV / VI / VII型细菌分泌系统基因簇位点和移动遗传元件上，包括整合和接合元件，预变性，I类整合子，IS元件和致病性/抗生素抵抗岛屿。 VRprofile因此能够使用HMMer或BLASTp搜索共同定位这些保守基因簇的同源物。随着同源基因簇搜索模块与序列组成模块的整合，VRprofile比其他广泛使用的方法显示出更好的岛状区域预测性能。此外，VRprofile还提供了一个集成的Web界面，可将识别的基因簇与MobilomeDB归档的基因簇或各种细菌基因组进行对齐和可视化。 VRprofile可能有助于满足对细菌可变区重新注释的日益增长的需求，并有助于实时定义感兴趣致病菌中疾病相关基因簇。

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. 

https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbw141/2888442?redirectedFrom=fulltext