TY - JOUR
T1 - Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks
AU - Ceol, Arnaud
AU - Montanari, Piero
AU - Bartolini, Ilaria
AU - Ceri, Stefano
AU - Ciaccia, Paolo
AU - Patella, Marco
AU - Masseroli, Marco
N1 - Funding Information:
This work was supported by the ERC Advanced Grant 693174 “Data-Driven Genomic Computing (GeCo)” project (2016-2021), funded by the European Research Council, which covered also the publication costs. The funding body did not have any role in the design of the study and in the collection, analysis and interpretation of the data, as well as in writing the manuscript. This work was also partially supported by the Italian Ministry of Health with Ricerca Corrente and 5x1000 funds. Acknowledgements
Publisher Copyright:
© 2020, The Author(s).
Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2020/12/1
Y1 - 2020/12/1
N2 - Background: 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. Results: 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. Conclusions: 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/.
AB - Background: 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. Results: 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. Conclusions: 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/.
KW - Computational genomics
KW - Genome browser
KW - Genome-wide pattern-search
KW - Visual analytics
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U2 - 10.1186/s12859-020-03781-2
DO - 10.1186/s12859-020-03781-2
M3 - Article
C2 - 33076821
AN - SCOPUS:85092772888
VL - 21
JO - BMC Bioinformatics
JF - BMC Bioinformatics
SN - 1471-2105
IS - 1
M1 - 464
ER -