{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T03:42:45Z","timestamp":1770435765948,"version":"3.49.0"},"reference-count":101,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: MicroRNAs (miRNAs) are important regulators of biological processes in plants and animals. Recently, miRNA genes have been discovered, whose primary transcripts are spliced and which cannot be predicted directly from genomic sequence. Hence, more sophisticated programs for the detection of spliced miRNAs are required.<\/jats:p><jats:p>Results: Here, we present the first method for the prediction of spliced miRNAs in plants. For a given genomic sequence, SplamiR creates a database of complementary sequence pairs, which might encode for RNAs folding into stem\u2013loop structures. Next, in silico splice variants of database sequences with complementarity to an mRNA of interest are classified as to whether they could represent miRNAs targeting this mRNA. Our method identifies all known cases of spliced miRNAs in rice, and a previously undiscovered miRNA in maize which is supported by an expressed sequence tag (EST). SplamiR permits identification of spliced miRNAs for a given target mRNA in many plant genomes.<\/jats:p><jats:p>Availability: The program is freely available at http:\/\/www.uni-jena.de\/SplamiR.html.<\/jats:p><jats:p>Contact: \u00a0guenter.theissen@uni-jena.de<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr132","type":"journal-article","created":{"date-parts":[[2011,3,19]],"date-time":"2011-03-19T00:25:49Z","timestamp":1300494349000},"page":"1215-1223","source":"Crossref","is-referenced-by-count":16,"title":["SplamiR\u2014prediction of spliced miRNAs in plants"],"prefix":"10.1093","volume":"27","author":[{"given":"Christoph J.","family":"Thieme","sequence":"first","affiliation":[{"name":"Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lydia","family":"Gramzow","sequence":"additional","affiliation":[{"name":"Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dajana","family":"Lobbes","sequence":"additional","affiliation":[{"name":"Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"G\u00fcnter","family":"Thei\u00dfen","sequence":"additional","affiliation":[{"name":"Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,3,17]]},"reference":[{"key":"2023012512174777800_B1","doi-asserted-by":"crossref","first-page":"i313","DOI":"10.1093\/bioinformatics\/btp191","article-title":"Toward a gold standard for promoter prediction evaluation","volume":"25","author":"Abeel","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512174777800_B2","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1101\/gr.2908205","article-title":"Computational prediction of miRNAs in Arabidopsis thaliana","volume":"15","author":"Adai","year":"2005","journal-title":"Genome Res."},{"key":"2023012512174777800_B3","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.cell.2005.04.004","article-title":"microRNA-directed phasing during trans-acting siRNA biogenesis in plants","volume":"121","author":"Allen","year":"2005","journal-title":"Cell"},{"key":"2023012512174777800_B4","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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