{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T09:26:52Z","timestamp":1740130012970,"version":"3.37.3"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,5,11]],"date-time":"2020-05-11T00:00:00Z","timestamp":1589155200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["BA2168\/16-1","BA2168\/21-1","BA2168\/3-3"],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Germany\u2019s Excellence Strategy","award":["390939984","NCT3.0_2015.54"]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["Di1421\/9-1"],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"Abstract<\/jats:title>\n RNA molecules fold into complex structures as a result of intramolecular interactions between their nucleotides. The function of many non-coding RNAs and some cis-regulatory elements of messenger RNAs highly depends on their fold. Single-nucleotide variants (SNVs) and other types of mutations can disrupt the native function of an RNA element by altering its base pairing pattern. Identifying the effect of a mutation on an RNA\u2019s structure is, therefore, a crucial step in evaluating the impact of mutations on the post-transcriptional regulation and function of RNAs within the cell. Even though a single nucleotide variation can have striking impacts on the structure formation, interpreting and comparing the impact usually needs expertise and meticulous efforts. Here, we present MutaRNA, a web server for visualization and interpretation of mutation-induced changes on the RNA structure in an intuitive and integrative fashion. To this end, probabilities of base pairing and position-wise unpaired probabilities of wildtype and mutated RNA sequences are computed and compared. Differential heatmap-like dot plot representations in combination with circular plots and arc diagrams help to identify local structure abberations, which are otherwise hidden in standard outputs. Eventually, MutaRNA provides a comprehensive and comparative overview of the mutation-induced changes in base pairing potentials and accessibility. The MutaRNA web server is freely available at http:\/\/rna.informatik.uni-freiburg.de\/MutaRNA.<\/jats:p>","DOI":"10.1093\/nar\/gkaa331","type":"journal-article","created":{"date-parts":[[2020,4,22]],"date-time":"2020-04-22T19:09:43Z","timestamp":1587582583000},"page":"W287-W291","source":"Crossref","is-referenced-by-count":18,"title":["MutaRNA: analysis and visualization of mutation-induced changes in RNA structure"],"prefix":"10.1093","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0173-3009","authenticated-orcid":false,"given":"Milad","family":"Miladi","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"}]},{"given":"Martin","family":"Raden","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7901-4752","authenticated-orcid":false,"given":"Sven","family":"Diederichs","sequence":"first","affiliation":[{"name":"Division of Cancer Research, Department of Thoracic Surgery, Faculty of Medicine, German Cancer Consortium (DKTK), University of Freiburg, 79085\u00a0Freiburg, Germany"},{"name":"Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120\u00a0Heidelberg, Germany"}]},{"given":"Rolf","family":"Backofen","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany"},{"name":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,5,11]]},"reference":[{"key":"2020062614043502600_B1","doi-asserted-by":"crossref","first-page":"442","DOI":"10.15252\/emmm.201506055","article-title":"The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations","volume":"8","author":"Diederichs","year":"2016","journal-title":"EMBO Mol. 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