iSmaRT：一个用于全面分析小RNA测序数据的工具包。

iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data.

作者信息

Panero Riccardo, Rinaldi Antonio, Memoli Domenico, Nassa Giovanni, Ravo Maria, Rizzo Francesca, Tarallo Roberta, Milanesi Luciano, Weisz Alessandro, Giurato Giorgio

机构信息

Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.

Department of Molecular Biotechnology and Health Sciences, University of Torino, via Nizza 52, Torino, Italy.

出版信息

Bioinformatics. 2017 Mar 15;33(6):938-940. doi: 10.1093/bioinformatics/btw734.

DOI:10.1093/bioinformatics/btw734

PMID:28057684

Abstract

SUMMARY

The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT ( i ntegrative Sm all R NA T ool-kit), an automated pipeline to analyze smallRNA-Seq data.

AVAILABILITY AND IMPLEMENTATION

iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington's Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp://labmedmolge-1.unisa.it (User: iSmart - Password: password).

CONTACT

aweisz@unisa.it or ggiurato@unisa.it.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

由于小非编码RNA（sncRNAs）在许多生物学环境中发挥的多效性作用，对其生物学作用进行研究的兴趣日益增加。虽然有几种方法和工具可用于研究微小RNA（miRNAs），但只有少数关注新型sncRNAs类别，特别是PIWI相互作用RNA（piRNAs）。为克服这些限制，我们开发了iSmaRT（综合小RNA工具包），这是一种用于分析smallRNA-Seq数据的自动化流程。

可用性和实现方式

iSmaRT是一组生物信息学工具和自有算法，通过图形用户界面（GUI）相互连接。除了对miRNAs进行全面分析外，它还实现了特定的计算模块来分析piRNAs，预测新的piRNAs并识别其RNA靶标。这里使用从亨廷顿舞蹈症患者脑样本生成的一个smallRNA-Seq数据集来说明iSmaRT的性能，展示了该流程如何以快速且用户友好的方式对不同类别的sncRNAs进行全面分析。iSmaRT可从网页ftp://labmedmolge-1.unisa.it免费获取（用户名：iSmart - 密码：password）。