Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks.
Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks.
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DOI：
10.1186/s12859-020-03781-2
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发表时间：
2020-10-19
影响因子：
3
通讯作者：
Masseroli M
中科院分区：
文献类型：
--
作者：
Ceol A;Montanari P;Bartolini I;Ceri S;Ciaccia P;Patella M;Masseroli M
基因组浏览器广泛用于定位感兴趣的基因组区域，但它们的交互使用显然限于检查短基因组部分。理想的交互是在浏览器上提供区域模式，然后在整个基因组中提取出现这种模式的其他基因组区域，按相似性排序。我们开发了SimSearch，这是一种优化的模式搜索方法和集成基因组浏览器（IGB）的开源插件，用于查找与给定区域模式相似的基因组区域集。在大数据集上提供高效的可视化全基因组分析计算；该插件支持直观的用户交互，用于在IGB轨道上选择有趣的模式，并可视化计算出整个基因组中类似模式的出现情况。SimSearch还包括注释和丰富结果的功能，并通过快速加载存储库进行增强，其中包括来自ENCODE和Roadmap Epigenomics的许多表观基因组特征数据集。本文还包括一些用例来展示生物学兴趣的多个全基因组分析，这可以通过利用所提出的方法轻松执行。新颖的SimSearch方法为有效的全基因组模式搜索和可视化提供了创新的支持；它的相关性和实用性通过一些重要的生物学用例得到了证明。SimSearch IGB插件、文档和代码可在https://deib-geco.github.io/simsearch-app/和https://github.com/DEIB-GECO/simsearch-app/免费获得。
Genome browsers are widely used for locating interesting genomic regions, but their interactive use is obviously limited to inspecting short genomic portions. An ideal interaction is to provide patterns of regions on the browser, and then extract other genomic regions over the whole genome where such patterns occur, ranked by similarity. We developed SimSearch, an optimized pattern-search method and an open source plugin for the Integrated Genome Browser (IGB), to find genomic region sets that are similar to a given region pattern. It provides efficient visual genome-wide analytics computation in large datasets; the plugin supports intuitive user interactions for selecting an interesting pattern on IGB tracks and visualizing the computed occurrences of similar patterns along the entire genome. SimSearch also includes functions for the annotation and enrichment of results, and is enhanced with a Quickload repository including numerous epigenomic feature datasets from ENCODE and Roadmap Epigenomics. The paper also includes some use cases to show multiple genome-wide analyses of biological interest, which can be easily performed by taking advantage of the presented approach. The novel SimSearch method provides innovative support for effective genome-wide pattern search and visualization; its relevance and practical usefulness is demonstrated through a number of significant use cases of biological interest. The SimSearch IGB plugin, documentation, and code are freely available at https://deib-geco.github.io/simsearch-app/ and https://github.com/DEIB-GECO/simsearch-app/.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
从全基因组结合测定中推断出染色质结合的蛋白质复合物。
影响因子：
7
作者：
Giannopoulou EG;Elemento O
通讯作者：
Elemento O
DOI：
10.1093/bioinformatics/btp472
发表时间：
2009-10-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Nicol JW;Helt GA;Blanchard SG Jr;Raja A;Loraine AE
通讯作者：
Loraine AE
影响因子：
9.5
作者：
Thorvaldsdóttir H;Robinson JT;Mesirov JP
通讯作者：
Mesirov JP
影响因子：
7
作者：
Skinner, Mitchell E.;Uzilov, Andrew V.;Holmes, Ian H.
通讯作者：
Holmes, Ian H.