SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data
Roberto R S de Andrade, Maite F S Vaslin1
1Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), 21941-590 Rio de Janeiro, RJ, Brasil. maite@micro.ufrj.br.
Virology Journal
|March 11, 2014
Summary
A new software, SearchSmallRNA, simplifies viral genome assembly from next-generation sequencing (NGS) small RNA data. This free tool aids in virus discovery and sequencing without requiring bioinformatics expertise.
Area of Science:
- Bioinformatics
- Virology
- Genomics
Background:
- Next-generation parallel sequencing (NGS) enables viral pathogen identification via host small RNA sequencing.
- Viral genomes can be assembled from host immune products, bypassing virus enrichment steps.
- Bioinformatics challenges exist in mapping vast NGS data for viral genome reconstruction.
Purpose of the Study:
- To develop user-friendly software for viral genome assembly from NGS small RNA data.
- To provide a graphical interface that bypasses the need for command-line bioinformatics knowledge.
- To enable analysis of viral small interfering RNA (vsRNA) profiles.
Main Methods:
- Developed SearchSmallRNA software in JAVA with a graphical interface.
- Implemented a mapping algorithm comparing NGS reads to reference genomes with Hamming distance.
- Validated the software using NGS datasets from HIV and plant viruses.
Main Results:
- SearchSmallRNA successfully reconstructed whole viral genomes from NGS small RNA datasets.
- The software demonstrated high reliability in viral genome reconstruction.
- Analysis of vsRNA size distribution and features is supported.
Conclusions:
- SearchSmallRNA is a valuable, free, and accessible tool for virus sequencing and discovery.
- The software's graphical interface simplifies viral genome assembly from NGS data.
- It offers high reliability for reconstructing viral genomes.
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