SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data

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/.

Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

“…Recently, an easy-to-use graphical interface, SearchSmallRNA, became available to reconstruct viral genomes with high reliability using small RNA data from NGS. SearchSmallRNA bypasses the need of line command and basic bioinformatics knowledge (18). Commercial packages such as CLC Genomics Workbench and Geneious or open platforms such as Galaxy also provide user-friendly interfaces and simplify the use and parameterization of these tools.…”

Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

“…In addition to the global alteration of Gh-miRNAs during CLRDV infection, we observed a decrease in the frequency of 24-nt sRNA in the infected plant with an enrichment of 15 gypsy-and copia-like retrotransposon transcripts [52]. In contrast, the CLRDV viral siRNA profile during infection revealed a greater abundance of the 22-nt vsiRNAs [54]. Thus, cotton DCLs are anticipated to play an important role in the mediation of CLRDV:cotton interactions during this compatible infection.…”

Identification and characterization of a novel geminivirus with a monopartite genome infecting apple trees

“…The contigs obtained were subsequently screened for homologous sequences by BLASTN on the GenBank Virus Reference Sequence Database (ftp://ftp.ncbi.nlm.nih.gov/refseq/ release/viral/). Coverage and distribution of viral-specific siRNAs were determined using the program SearchSmallRNA (de Andrade & Vaslin, 2014) and AGV (GenBank accession number KM386645) as reference virus sequence.…”