Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), 21941-590 Rio de Janeiro, RJ, Brasil.
Virol J. 2014 Mar 7;11:45. doi: 10.1186/1743-422X-11-45.
Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge.
In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells.
The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes.
SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface.
SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/.
下一代平行测序（NGS）允许通过对感染宿主的小 RNA 进行测序来识别病毒病原体。因此，可以从宿主免疫反应产物中组装病毒基因组，而无需事先进行病毒富集、扩增或纯化。然而，对所获得的大量信息进行映射提出了一个生物信息学挑战。
为了避免需要行命令和基本的生物信息学知识，我们开发了一种具有图形界面的映射软件，用于从 NGS 获得的小 RNA 数据集组装病毒基因组。SearchSmallRNA 是使用 Java 语言版本 7 在 NetBeans IDE 7.1 软件中开发的。该程序还允许分析病毒小干扰 RNA（vsRNA）谱；提供感染细胞中产生的 vsRNA 的大小分布和其他特征的概述。
该程序在文库中存在的每个测序读之间执行比较与选定的参考基因组。显示汉明距离小于或等于允许错配的读将被选为阳性，并用于组装长核苷酸基因组序列。为了验证该软件，使用从 HIV 和两种植物病毒获得的 NGS 数据集进行了不同的分析，以重建病毒全基因组。
SearchSmallRNA 程序能够使用 NGS 小 RNA 数据集重建病毒基因组，具有高度可靠性，因此将成为病毒测序和发现的有价值工具。它对所有研究社区都是可访问且免费的，并且具有易于使用的图形界面的优势。
SearchSmallRNA 是用 Java 编写的，可以在 http://www.microbiologia.ufrj.br/ssrna/ 免费获得。
