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Given an established miRNA family system (e.g. the miRBase family organization), this paper addresses the problem of automatically and accurately classifying newly found miRNAs to their corresponding families by supervised learning techniques. Concretely, we propose an effective method, <jats:italic>miRFam<\/jats:italic>, which uses only primary information of pre-miRNAs or mature miRNAs and a multiclass SVM, to automatically classify miRNA genes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>An existing miRNA family system prepared by miRBase was downloaded online. We first employed <jats:italic>n<\/jats:italic>-grams to extract features from known precursor sequences, and then trained a multiclass SVM classifier to classify new miRNAs (i.e. their families are unknown). Comparing with miRBase's sequence alignment and manual modification, our study shows that the application of machine learning techniques to miRNA family classification is a general and more effective approach. When the testing dataset contains more than 300 families (each of which holds no less than 5 members), the classification accuracy is around 98%. Even with the entire miRBase15 (1056 families and more than 650 of them hold less than 5 samples), the accuracy surprisingly reaches 90%.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Based on experimental results, we argue that <jats:italic>miRFam<\/jats:italic> is suitable for application as an automated method of family classification, and it is an important supplementary tool to the existing alignment-based small non-coding RNA (sncRNA) classification methods, since it only requires primary sequence information.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Availability<\/jats:title>\n            <jats:p>The source code of <jats:italic>miRFam<\/jats:italic>, written in C++, is freely and publicly available at: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/admis.fudan.edu.cn\/projects\/miRFam.htm\" ext-link-type=\"uri\">http:\/\/admis.fudan.edu.cn\/projects\/miRFam.htm<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-216","type":"journal-article","created":{"date-parts":[[2011,5,28]],"date-time":"2011-05-28T06:26:20Z","timestamp":1306563980000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM"],"prefix":"10.1186","volume":"12","author":[{"given":"Jiandong","family":"Ding","sequence":"first","affiliation":[]},{"given":"Shuigeng","family":"Zhou","sequence":"additional","affiliation":[]},{"given":"Jihong","family":"Guan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,5,28]]},"reference":[{"issue":"9","key":"4571_CR1","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","volume":"25","author":"AM Waterhouse","year":"2009","unstructured":"Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ: Jalview Version 2-a multiple sequence alignment editor and analysis workbench. 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