Abstract
BackgroundNext-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.MethodsIn 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.ResultsThe 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.ConclusionsSearchSmallRNA 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.Availability and implementationSearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/.
Highlights
Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts
Availability and implementation: SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/
To bypass the need of this kind of expertise or knowledge, and to permit the mapping and assemblage of viral genomes using NGS datasets, we developed SearchSmallRNA, an easy-to-use software that does not require any knowledge of programming languages and can be used by all researchers
Summary
Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Antiviral silencing host pathways known as RNA interference (RNAi) can be triggered by the presence of viral double-stranded RNAs (dsRNA). These dsRNA structures are recognized and processed into vsRNAs that vary in length from 21 to 24 nucleotides. Researchers with bioinformatics expertise have become indispensable for virus genome mapping from NGS libraries data. To bypass the need of this kind of expertise or knowledge, and to permit the mapping and assemblage of viral genomes using NGS datasets, we developed SearchSmallRNA, an easy-to-use software that does not require any knowledge of programming languages and can be used by all researchers
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