相位罐：全基因组计算鉴定phasiRNAs及其调控级联

PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades.

作者信息

Guo Qingli, Qu Xiongfei, Jin Weibo

机构信息

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.

出版信息

Bioinformatics. 2015 Jan 15;31(2):284-6. doi: 10.1093/bioinformatics/btu628. Epub 2014 Sep 21.

DOI:10.1093/bioinformatics/btu628

PMID:25246430

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.

摘要

未标注

新出现的证据表明，阶段性小干扰RNA（phasiRNAs）是植物中重要的内源性调节因子。然而，用于phasiRNAs的综合预测工具仍然有限。在本文中，我们介绍了一个独立的软件包PhaseTank，用于系统地表征phasiRNAs及其调控网络。（i）它可以高灵敏度和特异性地识别phasiRNAs/tasiRNAs功能级联（miRNA/phasiRNA → PHAS位点 → phasiRNA → 靶标）。（ii）通过一次命令分析，它可以从任何给定序列生成预测的PHAS基因的全面注释和定量。（iii）PhaseTank对无限制生物体来源的序列同源性的先验信息没有限制。