Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2012

Open Access Research

VIRGO: visualization of A-to-I RNA editing sites in genomic sequences

Rosario Distefano1, Giovanni Nigita1, Valentina Macca1, Alessandro Laganà2, Rosalba Giugno3, Alfredo Pulvirenti3* and Alfredo Ferro3

Author Affiliations

1 Department of Mathematics and Computer Science - University of Catania, Catania, Italy

2 Department of Molecular Virology, Immunology and Medical Genetics Comprehensive Cancer Center - The Ohio State University, Ohio, USA

3 Department of Clinical and Molecular Biomedicine - University of Catania, Catania, Italy

For all author emails, please log on.

BMC Bioinformatics 2013, 14(Suppl 7):S5  doi:10.1186/1471-2105-14-S7-S5

Published: 22 April 2013

Abstract

Background

RNA Editing is a type of post-transcriptional modification that takes place in the eukaryotes. It alters the sequence of primary RNA transcripts by deleting, inserting or modifying residues. Several forms of RNA editing have been discovered including A-to-I, C-to-U, U-to-C and G-to-A. In recent years, the application of global approaches to the study of A-to-I editing, including high throughput sequencing, has led to important advances. However, in spite of enormous efforts, the real biological mechanism underlying this phenomenon remains unknown.

Description

In this work, we present VIRGO (http://atlas.dmi.unict.it/virgo/ webcite), a web-based tool that maps Ato-G mismatches between genomic and EST sequences as candidate A-to-I editing sites. VIRGO is built on top of a knowledge-base integrating information of genes from UCSC, EST of NCBI, SNPs, DARNED, and Next Generations Sequencing data. The tool is equipped with a user-friendly interface allowing users to analyze genomic sequences in order to identify candidate A-to-I editing sites.

Conclusions

VIRGO is a powerful tool allowing a systematic identification of putative A-to-I editing sites in genomic sequences. The integration of NGS data allows the computation of p-values and adjusted p-values to measure the mapped editing sites confidence. The whole knowledge base is available for download and will be continuously updated as new NGS data becomes available.