{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T05:19:52Z","timestamp":1784179192995,"version":"3.55.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Emerging evidence has revealed phased siRNAs (phasiRNAs) as important endogenous regulators in plants. However, the integrated prediction tools for phasiRNAs are still limited. In this article, we introduce a stand-alone package PhaseTank for systematically characterizing phasiRNAs and their regulatory networks. (i) It can identify phasiRNAs\/tasiRNAs functional cascades (miRNA\/phasiRNA\u2192 PHAS loci\u2192phasiRNA\u2192target) with high sensitivity and specificity. (ii) By one command analysis, it generates comprehensive annotation and quantification of the predicted PHAS genes from any given sequences. (iii) PhaseTank has no restriction with regards to prior information of sequence homology of unrestricted organism origins.<\/jats:p>\n               <jats:p>Availability and implementation: PhaseTank is a free and open-source tool. The package is available at http:\/\/phasetank.sourceforge.net\/ .<\/jats:p>\n               <jats:p>Contact: \u00a0weibojin@gmail.com or guoql.karen@gmail.com .<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu628","type":"journal-article","created":{"date-parts":[[2014,9,23]],"date-time":"2014-09-23T02:41:35Z","timestamp":1411440095000},"page":"284-286","source":"Crossref","is-referenced-by-count":74,"title":["PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades"],"prefix":"10.1093","volume":"31","author":[{"given":"Qingli","family":"Guo","sequence":"first","affiliation":[{"name":"1 College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 2 College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and 3 School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"},{"name":"1 College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 2 College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and 3 School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiongfei","family":"Qu","sequence":"additional","affiliation":[{"name":"1 College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 2 College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and 3 School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weibo","family":"Jin","sequence":"additional","affiliation":[{"name":"1 College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 2 College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and 3 School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"},{"name":"1 College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 2 College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and 3 School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,9,21]]},"reference":[{"key":"2023020116152062000_btu628-B1","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1093\/bioinformatics\/btn604","article-title":"CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets","volume":"25","author":"Addo-Quaye","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020116152062000_btu628-B2","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1016\/j.semcdb.2010.03.008","article-title":"miRNAs in the biogenesis of trans-acting siRNAs in higher plants","volume":"21","author":"Allen","year":"2010","journal-title":"Semin. 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