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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.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>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.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusions<\/jats:title>\n<jats:p>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 <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/deib-geco.github.io\/simsearch-app\/\">https:\/\/deib-geco.github.io\/simsearch-app\/<\/jats:ext-link> and <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/DEIB-GECO\/simsearch-app\/\">https:\/\/github.com\/DEIB-GECO\/simsearch-app\/<\/jats:ext-link>.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-020-03781-2","type":"journal-article","created":{"date-parts":[[2020,10,19]],"date-time":"2020-10-19T13:04:25Z","timestamp":1603112665000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks"],"prefix":"10.1186","volume":"21","author":[{"given":"Arnaud","family":"Ceol","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Piero","family":"Montanari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ilaria","family":"Bartolini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefano","family":"Ceri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo","family":"Ciaccia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Patella","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2574-1174","authenticated-orcid":false,"given":"Marco","family":"Masseroli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,10,19]]},"reference":[{"issue":"6","key":"3781_CR1","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/nrg.2016.49","volume":"17","author":"S Goodwin","year":"2016","unstructured":"Goodwin S, et al. 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Project home page: . Project source code and issue tracker: . Operating system(s): Platform independent. Programming language: Java 8. Other requirements: Integrated Genome Browser. License: The SimSearch IGB plugin is released under the Apache License 2.0; the pattern-search algorithm is copyrighted by the University of Bologna. Any restrictions to use by non-academics: The pattern-search algorithm is free for non-commercial use only","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Availability and requirement"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable (public data).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"464"}}