IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.
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Islandviewer 4：扩展了大规模数据集基因组岛的预测。
DOI：
10.1093/nar/gkx343
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发表时间：
2017-07-03
影响因子：
14.9
通讯作者：
Brinkman FSL
中科院分区：
文献类型：
--
作者：
Bertelli C;Laird MR;Williams KP;Simon Fraser University Research Computing Group;Lau BY;Hoad G;Winsor GL;Brinkman FSL
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细菌基因组中的基因组岛（GI，可能水平起源的区域）。地理标志不成比例地编码增强微生物在生态位内的适应性和竞争力的因子，包括毒力因子和其他医学或环境重要适应性。我们在这里报告IslandViewer 4的发布，其新功能可满足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，用户管理Web界面以及用于批量分析的HTTP API都提供了安全身份验证，以方便提交更多基因组和检索结果。此外，IslandViewer的集成GI预测从多种方法已得到改进和扩展，通过集成精确的Islander方法预先计算的基因组，以及更新的IslandPath-DIMOB预先计算和用户提供的自定义基因组分析。最后，包括毒力因子和抗生素耐药性在内的预先计算的预测现在可用于RefSeq中公开的6193个完整的细菌和古细菌菌株。IslandViewer 4提供了关键的增强功能，以促进地理标志的分析，并更好地了解它们在成功的环境微生物和病原体进化中的作用。
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.
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影响因子：
3
作者：
Waack S;Keller O;Asper R;Brodag T;Damm C;Fricke WF;Surovcik K;Meinicke P;Merkl R
通讯作者：
Merkl R
影响因子：
3
作者：
Langille MG;Hsiao WW;Brinkman FS
通讯作者：
Brinkman FS
影响因子：
5.1
作者：
Miyazaki, Ryo;Bertelli, Claire;van der Meer, Jan Roelof
通讯作者：
van der Meer, Jan Roelof
DOI：
10.1093/bioinformatics/btv376
发表时间：
2015-10-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Laird MR;Langille MG;Brinkman FS
通讯作者：
Brinkman FS
影响因子：
28.3
作者：
Ingle, Danielle J.;Tauschek, Marija;Holt, Kathryn E.
通讯作者：
Holt, Kathryn E.