Qingli Guo1, Xiongfei Qu2, Weibo Jin1. 1. 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. 2. 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.
Abstract
UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: PhaseTank is a free and open-source tool. The package is available at http://phasetank.sourceforge.net/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: PhaseTank is a free and open-source tool. The package is available at http://phasetank.sourceforge.net/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Sukumaran Sunitha; Rodrigo Loyola; José Antonio Alcalde; Patricio Arce-Johnson; José Tomás Matus; Christopher D Rock Journal: G3 (Bethesda) Date: 2019-03-07 Impact factor: 3.154