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

BMC Bioinformatics

Research

Rosalba Giugno¹  Alfredo Ferro¹  Alfredo Pulvirenti¹  Giovanni Nigita²  Valentina Macca²  Rosario Distefano²  Alessandro Laganà³ 

[1] Department of Clinical and Molecular Biomedicine, University of Catania, Catania, Italy;Department of Mathematics and Computer Science, University of Catania, Catania, Italy;Department of Molecular Virology, Immunology and Medical Genetics Comprehensive Cancer Center - The Ohio State University, Ohio, USA;

关键词: Next Generation Sequencing;    Editing Site;    Next Generation Sequencing Data;    Editing Event;    Adenosine Deaminase Acting;   

DOI  :  10.1186/1471-2105-14-S7-S5

来源: Springer

【 摘 要 】

BackgroundRNA 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.DescriptionIn this work, we present VIRGO (http://atlas.dmi.unict.it/virgo/), 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.ConclusionsVIRGO 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.

【 授权许可】

Unknown   
© Distefano et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.