{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T14:49:55Z","timestamp":1784731795442,"version":"3.55.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":470,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3\u2032-modifications (e.g. uridylation, adenylation), 5\u2032-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface.<\/jats:p>\n               <jats:p>Availability and implementation: Chimira has been developed as a web application and it is accessible here: http:\/\/www.ebi.ac.uk\/research\/enright\/software\/chimira.<\/jats:p>\n               <jats:p>Contact: \u00a0aje@ebi.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv380","type":"journal-article","created":{"date-parts":[[2015,6,21]],"date-time":"2015-06-21T00:00:20Z","timestamp":1434844820000},"page":"3365-3367","source":"Crossref","is-referenced-by-count":106,"title":["Chimira: analysis of small RNA sequencing data and microRNA modifications"],"prefix":"10.1093","volume":"31","author":[{"given":"Dimitrios M.","family":"Vitsios","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory\u2014European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anton J.","family":"Enright","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory\u2014European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,6,20]]},"reference":[{"key":"2023020202322953100_btv380-B1","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/nar\/gkt282","article-title":"BLAST: a more efficient report with usability improvements","volume":"41","author":"Boratyn","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020202322953100_btv380-B2","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1101\/gr.106054.110","article-title":"A comprehensive survey of 3\u2032 animal miRNA modification events and a possible role for 3\u2032 adenylation in modulating miRNA targeting effectiveness","volume":"20","author":"Burroughs","year":"2010","journal-title":"Genome Res."},{"key":"2023020202322953100_btv380-B3","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.ymeth.2013.06.027","article-title":"Kraken: a set of tools for quality control and analysis of high-throughput sequence data","volume":"63","author":"Davis","year":"2013","journal-title":"Methods"},{"key":"2023020202322953100_btv380-B4","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gkm952","article-title":"mirbase: tools for microrna genomics","volume":"36","author":"Griffiths-Jones","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023020202322953100_btv380-B5","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1016\/j.cell.2009.08.002","article-title":"TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation","volume":"138","author":"Heo","year":"2009","journal-title":"Cell"},{"key":"2023020202322953100_btv380-B6","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/j.cell.2012.09.022","article-title":"Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs","volume":"151","author":"Heo","year":"2012","journal-title":"Cell"},{"key":"2023020202322953100_btv380-B7","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"2023020202322953100_btv380-B8","doi-asserted-by":"crossref","first-page":"1878","DOI":"10.1093\/nar\/gkp031","article-title":"Adenylation of plant miRNAs","volume":"37","author":"Shanfa","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020202322953100_btv380-B9","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1186\/1752-0509-6-S2-S14","article-title":"MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues","volume":"6","author":"Li","year":"2012","journal-title":"BMC Syst. 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