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 ove

SUBMITTER: de Andrade RR 

PROVIDER: S-EPMC4007622 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature