TY - JOUR
T1 - VIRGO
T2 - Visualization of A-to-I RNA editing sites in genomic sequences
AU - Distefano, Rosario
AU - Nigita, Giovanni
AU - Macca, Valentina
AU - Laganà, Alessandro
AU - Giugno, Rosalba
AU - Pulvirenti, Alfredo
AU - Ferro, Alfredo
N1 - Funding Information:
We would like to thank the anonymous reviewers for their valuable comments. Funding: Valentina Macca has been supported by a fellowship sponsored by “Associazione Sclerosi Tuberosa”, A.S.T.
Funding Information:
The publication costs for this article were funded by PO - FESR 2007-2013 grant - CUP: G23F11000840004 -Title: “BIOWINE”. This article has been published as part of BMC Bioinformatics Volume 14 Supplement 7, 2013: Italian Society of Bioinformatics (BITS): Annual Meeting 2012. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcbioinformatics/supplements/14/S7 1Department of Mathematics and Computer Science - University of Catania, Catania, Italy. 2Department of Molecular Virology, Immunology and Medical Genetics Comprehensive Cancer Center - The Ohio State University, Ohio, USA. 3Department of Clinical and Molecular Biomedicine - University of Catania, Catania, Italy.
PY - 2013/4/22
Y1 - 2013/4/22
N2 - 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/), 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.
AB - 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/), 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.
UR - https://www.scopus.com/pages/publications/84887170034
U2 - 10.1186/1471-2105-14-S7-S5
DO - 10.1186/1471-2105-14-S7-S5
M3 - Article
C2 - 23815474
AN - SCOPUS:84887170034
SN - 1471-2105
VL - 14
JO - BMC Bioinformatics
JF - BMC Bioinformatics
IS - SUPPL7
M1 - S5
ER -