{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,5]],"date-time":"2025-08-05T12:18:16Z","timestamp":1754396296557},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We describe miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis\u2014the analysis of 3\u2032 modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA is implemented in Python (version 3) and employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes miRBase, currently version 21, as a source of known microRNAs for analysis. miTRATA notifies user(s) via email to download as well as visualize the results online. miTRATA\u2019s strengths lie in (i) its biologist-focused web interface, (ii) improved scalability via parallel processing and (iii) its uniqueness as a webtool to perform microRNA truncation and tailing analysis.<\/jats:p>\n               <jats:p>Availability and implementation: miTRATA is developed in Python and PHP. It is available as a web-based application from https:\/\/wasabi.dbi.udel.edu\/\u223capps\/ta\/.<\/jats:p>\n               <jats:p>Contact: \u00a0meyers@dbi.udel.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv583","type":"journal-article","created":{"date-parts":[[2015,10,11]],"date-time":"2015-10-11T01:19:15Z","timestamp":1444526355000},"page":"450-452","source":"Crossref","is-referenced-by-count":19,"title":["miTRATA: a web-based tool for <i>mi<\/i>croRNA <i>Tr<\/i>uncation <i>a<\/i>nd <i>T<\/i>ailing <i>A<\/i>nalysis"],"prefix":"10.1093","volume":"32","author":[{"given":"Parth","family":"Patel","sequence":"first","affiliation":[{"name":"1 Center for Bioinformatics and Computational Biology and"},{"name":"2 Delaware Biotechnology Institute and"}]},{"given":"S. Deepthi","family":"Ramachandruni","sequence":"additional","affiliation":[{"name":"2 Delaware Biotechnology Institute and"}]},{"given":"Atul","family":"Kakrana","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics and Computational Biology and"},{"name":"2 Delaware Biotechnology Institute and"}]},{"given":"Mayumi","family":"Nakano","sequence":"additional","affiliation":[{"name":"3 Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA"}]},{"given":"Blake C.","family":"Meyers","sequence":"additional","affiliation":[{"name":"2 Delaware Biotechnology Institute and"},{"name":"3 Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA"}]}],"member":"286","published-online":{"date-parts":[[2015,10,10]]},"reference":[{"key":"2023020110313176000_btv583-B1","doi-asserted-by":"crossref","first-page":"5270","DOI":"10.1093\/nar\/gku157","article-title":"A non-canonical plant microRNA target site","volume":"42","author":"Brousse","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020110313176000_btv583-B2","doi-asserted-by":"crossref","first-page":"e63","DOI":"10.1093\/nar\/gkv537","article-title":"Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs","volume":"43","author":"Chou","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2023020110313176000_btv583-B3","doi-asserted-by":"crossref","first-page":"e139","DOI":"10.1093\/nar\/gku693","article-title":"sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets,including new miRNA target-identification software","volume":"43","author":"Kakrana","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020110313176000_btv583-B4","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1093\/nar\/gkt1181","article-title":"miRBase: annotating high confidence microRNAs using deep sequencing data","volume":"42","author":"Kozomara","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020110313176000_btv583-B5","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1016\/j.cub.2005.07.029","article-title":"Methylation protects miRNAs and siRNAs from a 3\u2032-end uridylation activity in Arabidopsis","volume":"15","author":"Li","year":"2005","journal-title":"Curr. 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