IslandViewer 4：用于更大规模数据集的基因组岛的扩展预测。

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.

机构信息

Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

出版信息

Nucleic Acids Res. 2017 Jul 3;45(W1):W30-W35. doi: 10.1093/nar/gkx343.

DOI:10.1093/nar/gkx343

PMID:28472413

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5570257/

Abstract

IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.

摘要

IslandViewer（http://www.pathogenomics.sfu.ca/islandviewer/）是一个广泛使用的网络服务器，用于预测和交互式可视化细菌和古菌基因组中的基因组岛（GI，可能水平起源的区域）。GI 不成比例地编码增强微生物在特定生态位中的适应性和竞争力的因素，包括毒力因子和其他医学或环境重要的适应性。我们在此报告 IslandViewer 4 的发布，具有新的功能来适应更大规模微生物基因组学分析的需求，同时扩展 GI 预测并改进其灵活的可视化界面。现在提供了用户管理 Web 界面和用于批量分析的 HTTP API，并通过安全认证来促进提交更多数量的基因组和检索结果。此外，通过集成用于预计算基因组的精确 Islander 方法，以及用于预计算和用户提供的自定义基因组分析的更新的 IslandPath-DIMOB，IslandViewer 的集成 GI 预测从多种方法得到了改进和扩展。最后，现在为 RefSeq 中公开的 6193 个完整细菌和古菌菌株提供了包括毒力因子和抗微生物药物耐药性的预计算预测。IslandViewer 4 提供了关键的增强功能，以促进 GI 的分析，并更好地理解它们在成功环境微生物和病原体进化中的作用。