{"id":572,"date":"2013-06-26T23:32:12","date_gmt":"2013-06-26T21:32:12","guid":{"rendered":"http:\/\/bioinfo2.ugr.es\/ceUGR\/?page_id=572"},"modified":"2020-09-17T02:05:26","modified_gmt":"2020-09-17T00:05:26","slug":"miranalyzer","status":"publish","type":"page","link":"https:\/\/bioinfo2.ugr.es\/ceUGR\/miranalyzer\/","title":{"rendered":"miRanalyzer"},"content":{"rendered":"<h4><em><strong>**Please note that miRanalyzer was replaced by the newer, easier and more complete software <a href=\"https:\/\/arn.ugr.es\/srnatoolbox\/srnabench\/\">sRNAbench<\/a>. Old miRanalyzer versions are no longer supported. miRanalyzer users are encouraged to use <a href=\"https:\/\/arn.ugr.es\/srnatoolbox\/srnabench\/\">sRNAbench<\/a> instead.<\/strong><\/em><\/h4>\n<p>Websites:<\/p>\n<ul>\n<li><a href=\"http:\/\/www.google.com\/url?q=http%3A%2F%2Fbioinfo5.ugr.es%2FmiRanalyzer_dev%2FmiRanalyzer.php&amp;sa=D&amp;sntz=1&amp;usg=AFQjCNFC_Q1Vo_up3OBregr6HjxhWAvgzg\" target=\"_blank\" rel=\"noopener noreferrer\">miRanalyzer beta<\/a><\/li>\n<li><a href=\"http:\/\/www.google.com\/url?q=http%3A%2F%2Fbioinfo5.ugr.es%2FmiRanalyzer%2FmiRanalyzer.php&amp;sa=D&amp;sntz=1&amp;usg=AFQjCNHNTuU3zl0-navrjuxxhcPzWY0bBg\" target=\"_blank\" rel=\"noopener noreferrer\">Old version<\/a><\/li>\n<\/ul>\n<p>Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we developed miRanalyzer, a web server tool for the analysis of deep-sequencing experiments for small RNAs. The web server tool requires a simple input file containing a list of unique reads and its copy numbers (expression levels). Using these data, miRanalyzer (i) detects all known microRNA sequences annotated in miRBase, (ii) finds all perfect matches against other libraries of transcribed sequences and (iii) predicts new microRNAs. The prediction of new microRNAs is an especially important point as there are many species with very few known microRNAs. Therefore, we implemented a highly accurate machine learning algorithm for the prediction of new microRNAs that reaches AUC values of 97.9% and recall values of up to 75% on unseen data. The web tool summarizes all the described steps in a single output page, which provides a comprehensive overview of the analysis, adding links to more detailed output pages for each analysis module. miRanalyzer is available at http:\/\/web.bioinformatics.cicbiogune.es\/microRNA\/.<\/p>\n<p><span style=\"font-family: book antiqua,palatino;\">Hackenberg, M., Sturm, M., Langenberger, D., Falcon-Perez, J.M. and Aransay, A.M. (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments, Nucleic acids research, 37, W68-76. <\/span><span style=\"font-family: book antiqua,palatino;\"><a href=\"http:\/\/bioinfo5.ugr.es\/%7Emichael\/miRanalyzer_2009.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">PDF<\/a> <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19433510\" target=\"_blank\" rel=\"noopener noreferrer\">PubMed<\/a><\/span><\/p>\n<p><span style=\"font-family: book antiqua,palatino;\">Hackenberg, M., Rodriguez-Ezpeleta, N. and Aransay, A.M. (2011) miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments, Nucleic acids research, 39, W132-138. <a href=\"http:\/\/bioinfo5.ugr.es\/%7Emichael\/miRanalyzer_2011.pdf\">PDF<\/a> <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21515631\" target=\"_blank\" rel=\"noopener noreferrer\">PubMed<\/a><\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>**Please note that miRanalyzer was replaced by the newer, easier and more complete software sRNAbench. Old miRanalyzer versions are no longer supported. miRanalyzer users are encouraged to use sRNAbench instead. Websites: miRanalyzer beta Old version Next-generation sequencing allows now the &hellip;<\/p>\n<p class=\"read-more\"> <a class=\"more-link\" href=\"https:\/\/bioinfo2.ugr.es\/ceUGR\/miranalyzer\/\"> <span class=\"screen-reader-text\">miRanalyzer<\/span> Read More &raquo;<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":22,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/pages\/572"}],"collection":[{"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/comments?post=572"}],"version-history":[{"count":5,"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/pages\/572\/revisions"}],"predecessor-version":[{"id":1428,"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/pages\/572\/revisions\/1428"}],"wp:attachment":[{"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/media?parent=572"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}