title: SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
  
  
  METHODS
  SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/.
authors.forename: Roberto R S
authors.initials: RR
authors.lastname: de Andrade
authors.affiliation: Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), 21941-590 Rio de Janeiro, RJ, Brasil. maite@micro.ufrj.br.
authors.forename: Maite F S
authors.initials: MF
authors.lastname: Vaslin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D015723:Gene Library; D016679:Genome, Viral; D006678:HIV / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D010942:Plant Viruses / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D017421:Sequence Analysis / Q000379:methods*; D014773:Virology / Q000379:methods
chemical_list: D058727:RNA, Small Untranslated; D012367:RNA, Viral