IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.
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2015 Jul 1;43(W1):W104-8. doi: 10.1093/nar/gkv401. Epub
2015 Apr 27.IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 4.1Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.2M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.3Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada.4Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada brinkman@sfu.ca.AbstractIslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial resistance and virulence. We now report a major new release of IslandViewer, since the last release in 2013. IslandViewer 3 incorporates a completely new genome visualization tool, IslandPlot, enabling for the first time interactive genome analysis and gene search capabilities using synchronized circular, horizontal and vertical genome views. In addition, more curated virulence factors and antimicrobial resistance genes have been incorporated, and homologs of these genes identified in closely related genomes using strict filters. Pathogen-associated genes have been re-calculated for all pre-computed complete genomes. For user-uploaded genomes to be analysed, IslandViewer 3 can also now handle incomplete genomes, with an improved queuing system on compute nodes to handle user demand. Overall, IslandViewer 3 represents a significant new version of this GI analysis software, with features that may make it more broadly useful for general microbial genome analysis and visualization. (C) The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.PMID:
[PubMed - indexed for MEDLINE] PMCID: PMC4489224 IslandViewer 3 results page for Salmonella enterica subsp. enterica serovar Typhi str. Ty2 (accession number NC_). Panel (A) is the circular genome view, panel (B) is the vertical view with text descriptions of genes and gene products and panel (C) is the horizontal view to enable users to zoom in/out of regions of interest. Within each panel, GI predictions are represented as blocks (integrated results in red, IslandPick in green, SIGI-HMM in orange and IslandPath-DIMOB in blue), virulence genes (purple for curated, light purple for homologs), antimicrobial resistance genes (pink for curated, light pink for homologs) and pathogen-associated genes (orange) as circular glyphs. The legend can be used to turn individual items on/off in the circular view. Users can click on any island or double-click on any other region of panel (A), which will then zoom-in to those regions in panels (B) and (C) for more details. New in the toolbox, users can now search for a particular gene of interest and save a customized view.Nucleic Acids Res. 2015 July 1;43(Web Server issue):W104-W108.Publication TypesMeSH TermsSubstancesGrant SupportFull Text Sources
Supplemental Content
External link. Please review our .IslandViewer update: improved genomic island discovery and visualizationNucleic Acids ResB. K. Dhillon& T. A. Chiu& M. R. Laird& M. G. Langille& F. S. Brinkman
IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a web-accessible application for the computational prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin and are of high interest because they disproportionately encode virulence factors and other adaptations of medical, environmental and industrial interest. Many computational tools exist for the prediction of GIs, but three of the most accurate methods are available in integrated form via IslandViewer: IslandPath-DIMOB, SIGI-HMM and IslandPick. IslandViewer GI predictions are precomputed for all complete microbial genomes from National Center for Biotechnology Information, with an option to upload other genomes and/or perform customized analyses using different settings. Here, we report recent changes to the IslandViewer framework that have vastly improved its efficiency in handling an increasing number of users, plus better facilitate custom genome analyses. Users may also now overlay additional annotations such as virulence factors, antibiotic resistance genes and pathogen-associated genes on top of current GI predictions. Comparisons of GIs between user-selected genomes are now facilitated through a highly requested side-by-side viewer. IslandViewer improvements aim to provide a more flexible interface, coupled with additional highly relevant annotation information, to aid analysis of GIs in diverse microbial species.
IslandViewer更新：改进的基因组岛发现和可视化
IslandViewer（http://pathogenomics.sfu.ca/islandviewer）是用于细菌和古细菌基因组中基因组岛（Genomic Islands，GIs）计算预测和分析的一个网络可访问的应用程序。GIs是可能水平起源的基因簇，因为它们不成比例地编码毒力因子及对医学、环境和工业兴趣的适应，它们受到高度关注。存在许多进行GIs预测的计算工具，但是最准确的三种方法以整合的形式通过IslandViewer可用：IslandPath-DIMOB、SIGI-HMM和IIslandPick。IslandViewer GI预测预计算了来自国家生物技术信息中心（NCBI）的所有微生物基因组，具有一个上传其他基因组和/或使用不同设置执行定制分析的选项。这里，我们报道了IslandViewer框架的最新变化，它极大地增加了处理越来越多用户的效率，加上更好地促进了定制基因组分析。用户现在也可能在当前GI预测之上叠加额外的注释，例如毒力因子、抗生素抗性基因和病原体相关基因。用户挑选的基因组间GIs的比较现在通过一个高请求的并列查看器而促进。IslandViewer改进旨在提供一个更灵活的界面，连同额外高度相关的注释信息，以辅助不同微生物物种中的GIs分析。
10.1093/nar/gkt394http://nar.oxfordjournals.org/content/early//nar.gkt394.full.pdf1, Detecting genomic islands using bioinformatics approaches []
2, Genomic islands in pathogenic and environmental microorganisms []
3, Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes []
4, Pathogenicity islands and the evolution of microbes []
5, Horizontal gene transfer: sustaining pathogenicity and optimizing host-pathogen interactions []
6, The association of virulence factors with genomic islands []
7, Genomic islands: tools of bacterial horizontal gene transfer and evolution []
8, Burkholderia pseudomallei genome plasticity associated with genomic island variation []
9, IslandViewer: an integrated interface for computational identification and visualization of genomic islands []
10, Evaluation of genomic island predictors using a comparative genomics approach []
11, Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models []
12, IslandPath: aiding detection of genomic islands in prokaryotes []
13, GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects []
14, GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences []
15, An Integrative Approach for Genomic Island Prediction in Prokaryotic Genomes [http://dx.doi.org/10.-642-]
16, EGID: an ensemble algorithm for improved genomic island detection in genomic sequences []
17, Prediction of genomic islands in seven human pathogens using the Z-Island method []
18, MicrobeDB: a locally maintainable database of microbial genomic sequences []
19, Circos: an information aesthetic for comparative genomics []
20, VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors []
21, ARDB--Antibiotic Resistance Genes Database []
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现在时间是 02-17 04:24IslandViewer update: improved genomic island discovery and visualizationNucleic Acids ResB. K. Dhillon& T. A. Chiu& M. R. Laird& M. G. Langille& F. S. Brinkman
IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a web-accessible application for the computational prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin and are of high interest because they disproportionately encode virulence factors and other adaptations of medical, environmental and industrial interest. Many computational tools exist for the prediction of GIs, but three of the most accurate methods are available in integrated form via IslandViewer: IslandPath-DIMOB, SIGI-HMM and IslandPick. IslandViewer GI predictions are precomputed for all complete microbial genomes from National Center for Biotechnology Information, with an option to upload other genomes and/or perform customized analyses using different settings. Here, we report recent changes to the IslandViewer framework that have vastly improved its efficiency in handling an increasing number of users, plus better facilitate custom genome analyses. Users may also now overlay additional annotations such as virulence factors, antibiotic resistance genes and pathogen-associated genes on top of current GI predictions. Comparisons of GIs between user-selected genomes are now facilitated through a highly requested side-by-side viewer. IslandViewer improvements aim to provide a more flexible interface, coupled with additional highly relevant annotation information, to aid analysis of GIs in diverse microbial species.
IslandViewer更新：改进的基因组岛发现和可视化
IslandViewer（http://pathogenomics.sfu.ca/islandviewer）是用于细菌和古细菌基因组中基因组岛（Genomic Islands，GIs）计算预测和分析的一个网络可访问的应用程序。GIs是可能水平起源的基因簇，因为它们不成比例地编码毒力因子及对医学、环境和工业兴趣的适应，它们受到高度关注。存在许多进行GIs预测的计算工具，但是最准确的三种方法以整合的形式通过IslandViewer可用：IslandPath-DIMOB、SIGI-HMM和IIslandPick。IslandViewer GI预测预计算了来自国家生物技术信息中心（NCBI）的所有微生物基因组，具有一个上传其他基因组和/或使用不同设置执行定制分析的选项。这里，我们报道了IslandViewer框架的最新变化，它极大地增加了处理越来越多用户的效率，加上更好地促进了定制基因组分析。用户现在也可能在当前GI预测之上叠加额外的注释，例如毒力因子、抗生素抗性基因和病原体相关基因。用户挑选的基因组间GIs的比较现在通过一个高请求的并列查看器而促进。IslandViewer改进旨在提供一个更灵活的界面，连同额外高度相关的注释信息，以辅助不同微生物物种中的GIs分析。
10.1093/nar/gkt394http://nar.oxfordjournals.org/content/early//nar.gkt394.full.pdf1, Detecting genomic islands using bioinformatics approaches []
2, Genomic islands in pathogenic and environmental microorganisms []
3, Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes []
4, Pathogenicity islands and the evolution of microbes []
5, Horizontal gene transfer: sustaining pathogenicity and optimizing host-pathogen interactions []
6, The association of virulence factors with genomic islands []
7, Genomic islands: tools of bacterial horizontal gene transfer and evolution []
8, Burkholderia pseudomallei genome plasticity associated with genomic island variation []
9, IslandViewer: an integrated interface for computational identification and visualization of genomic islands []
10, Evaluation of genomic island predictors using a comparative genomics approach []
11, Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models []
12, IslandPath: aiding detection of genomic islands in prokaryotes []
13, GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects []
14, GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences []
15, An Integrative Approach for Genomic Island Prediction in Prokaryotic Genomes [http://dx.doi.org/10.-642-]
16, EGID: an ensemble algorithm for improved genomic island detection in genomic sequences []
17, Prediction of genomic islands in seven human pathogens using the Z-Island method []
18, MicrobeDB: a locally maintainable database of microbial genomic sequences []
19, Circos: an information aesthetic for comparative genomics []
20, VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors []
21, ARDB--Antibiotic Resistance Genes Database []
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