IslandViewer:细菌基因组中基因组岛鉴定的可视化界面

摘 要:

目前开发了几种计算方法来预测基因岛,这些计算方法或者利用序列组成偏倚方法,或者利用比较基因组学方法。IslandViewer是一个网络化可访问应用程序,它首次提供了用户友好的界面以使用最准确的基因组岛预测方法获得预计算的基因岛预测。图形界面允许以多种格式,在染色体和基因组水平上进行基因岛预测数据的查看和下载。

关键词: ,

基因岛(很可能是来源于水平转移的基因簇)在医学上重要的细菌适应中起着关键的作用。最近,开发了几种计算方法来预测基因岛,这些计算方法或者利用序列组成偏倚方法,或者利用比较基因组学方法。IslandViewer是一个网络化可访问应用程序,它首次提供了用户友好的界面以使用最准确的基因组岛预测方法(IslandPick、IslandPath-DIMOB和SIGI-HMM)获得预计算的基因岛预测,或者从用户输入的序列中进行预测。图形界面允许以多种格式,在染色体和基因组水平上容易地进行方法特异的或重叠的基因岛预测数据的查看和下载。

可用性:IslandViewer的网络网址:http://www.pathogenomics.sfu.ca/islandviewer,源码在遵循GNU GPL许可证下可免费获得。

IslandViewer:细菌基因组中基因组岛鉴定的可视化界面

IslandViewer: an integrated interface for computational identification and visualization of genomic islands.

Abstract: Genomic islands (clusters of genes of probable horizontal origin; GIs) play a critical role in medically important adaptations of bacteria. Recently, several computational methods have been developed to predict GIs that utilize either sequence composition bias or comparative genomics approaches. IslandViewer is a web accessible application that provides the first user-friendly interface for obtaining precomputed GI predictions, or predictions from user-inputted sequence, using the most accurate methods for genomic island prediction: IslandPick, IslandPath-DIMOB and SIGI-HMM. The graphical interface allows easy viewing and downloading of island data in multiple formats, at both the chromosome and gene level, for method-specific, or overlapping, GI predictions.

AVAILABILITY: The IslandViewer web service is available at http://www.pathogenomics.sfu.ca/islandviewer and the source code is freely available under the GNU GPL license.

参考文献:

Langille MG1, Brinkman FS. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics. 2009,25(5):664-5. doi: 10.1093/bioinformatics/btp030.

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