{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T03:02:46Z","timestamp":1770433366032,"version":"3.49.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: MicroRNAs (miRNAs) are important regulatory molecules. A critical step in elucidating miRNA function is identifying potential miRNA targets. However, few reliable tools have been developed for identifying miRNA targets in plants.<\/jats:p>\n               <jats:p>Results: Here, we developed a Smith\u2013Waterman-like alignment tool in order to accurately predict miRNA targets. Dynamic programming was used to build a score matrix based on the complementarity of nucleotides in order to trace the optimal local alignments. Important parameters, such as maximum mismatches and maximum consecutive mismatches between miRNAs and their targets, were also used for filtering the optimal local alignments. Almost all of the parameters in this alignment tool can be adjusted by users. Compared to other target prediction tools, Target-align exhibits strong sensitivity and accuracy for identifying miRNA targets. More importantly, Target-align can identify multi-target sites as well potential for non-cleaved targets sites by change the default settings. Windows, web and command-line versions were developed to better serve different users.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.leonxie.com\/targetAlign.php.<\/jats:p>\n               <jats:p>Contact: \u00a0zhangb@ecu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq568","type":"journal-article","created":{"date-parts":[[2010,10,19]],"date-time":"2010-10-19T04:15:50Z","timestamp":1287461750000},"page":"3002-3003","source":"Crossref","is-referenced-by-count":71,"title":["Target-align: a tool for plant microRNA target identification"],"prefix":"10.1093","volume":"26","author":[{"given":"Fuliang","family":"Xie","sequence":"first","affiliation":[{"name":"Department of Biology, East Carolina University, Greenville, NC 27858, USA"}]},{"given":"Baohong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biology, East Carolina University, Greenville, NC 27858, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,10,7]]},"reference":[{"key":"2023012507523936100_B1","doi-asserted-by":"crossref","first-page":"1566","DOI":"10.1093\/bioinformatics\/btq233","article-title":"TAPIR, a web server for the prediction of plant microRNA targets, including target mimics","volume":"26","author":"Bonnet","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012507523936100_B2","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1126\/science.1159151","article-title":"Widespread translational inhibition by plant miRNAs and siRNAs","volume":"320","author":"Brodersen","year":"2008","journal-title":"Science"},{"key":"2023012507523936100_B3","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":"2023012507523936100_B4","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.cell.2008.02.033","article-title":"Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation","volume":"133","author":"Montgomery","year":"2008","journal-title":"Cell"},{"key":"2023012507523936100_B5","doi-asserted-by":"crossref","first-page":"1602","DOI":"10.1101\/gr.080127.108","article-title":"Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening","volume":"18","author":"Moxon","year":"2008","journal-title":"Genome Res."},{"key":"2023012507523936100_B6","doi-asserted-by":"crossref","first-page":"2252","DOI":"10.1093\/bioinformatics\/btn428","article-title":"A toolkit for analysing large-scale plant small RNA datasets","volume":"24","author":"Moxon","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012507523936100_B7","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1016\/S0092-8674(02)00863-2","article-title":"Prediction of plant microRNA targets","volume":"110","author":"Rhoades","year":"2002","journal-title":"Cell"},{"key":"2023012507523936100_B8","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/j.devcel.2005.01.018","article-title":"Specific effects of microRNAs on the plant transcriptome","volume":"8","author":"Schwab","year":"2005","journal-title":"Dev. 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Chem."},{"key":"2023012507523936100_B12","doi-asserted-by":"crossref","first-page":"W701","DOI":"10.1093\/nar\/gki383","article-title":"miRU: an automated plant miRNA target prediction server","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/23\/3002\/48851003\/bioinformatics_26_23_3002.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/23\/3002\/48851003\/bioinformatics_26_23_3002.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:52:48Z","timestamp":1674633168000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/23\/3002\/221071"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,10,7]]},"references-count":12,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2010,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq568","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,12,1]]},"published":{"date-parts":[[2010,10,7]]}}}