title: PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades.
abstract: 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 → PHAS loci → phasiRNA → target) 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.
  
  
  METHODS
  PhaseTank is a free and open-source tool. The package is available at http://phasetank.sourceforge.net/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Qingli
authors.initials: Q
authors.lastname: Guo
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Xiongfei
authors.initials: X
authors.lastname: Qu
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Jin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D010944:Plants / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D012984:Software
chemical_list: D034741:RNA, Small Interfering