VIRGO
Visualization of A-to-I RNA editing sites in genomic sequences
••• AboutDocumentationStatisticsAdd new editing sitesDownload (VIRGO dataset) •••

By using VIRGO you can identify Adenosine-to-Inosine (A-to-I) RNA editing sites into genomic sequences. Once you submit DNA sequences, VIRGO will analyze them and will highlight putative A-to-I RNA Editing sites. Remember, the database keeps the correct positions of each mismatch. If you specify a wrong starting and/or ending position for the sequence, VIRGO will show, anyway, the right positions for the markers.
Find A-to-I RNA Editing Sites
Please insert your email address, before running the application if you want to be notified when your job is done.
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You can upload a file in FASTA like headers related to a group of related sequences. See the input format (for a good consultation, upload maximum 10-15 sequences; for a quickly processing, maximum sequence length: 80.000 nt, click here for input file example)
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input file example
Virgo example
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References
If you use VIRGO please cite the following work:
Rosario Distefano, Giovanni Nigita, Valentina Macca, Alessandro Laganà, Rosalba Giugno,
Alfredo Pulvirenti, Alfredo Ferro
"VIRGO: Visualization of A-to-I RNA editing sites in genomic sequences",
BMC Bioinformatics 2013, 14(Suppl 7):S5 doi:10.1186/1471-2105-14-S7-S5

For any question or comment please contact:
Alfredo Pulvirenti » apulvirenti@dmi.unict.it
Rosario Distefano » rosario.distefano.ict@gmail.com
Gianni Nigita » nigita@dmi.unict.it
Useful links
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Project members contact information
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Rosario Distefano
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Project Developer & Manager
Rosario Distefano
Master Degree in Computer Science
Heterogeneous Computing, Bioinformatics
Department of Mathematics and Computer Science
University of Catania, Italy[ Linkedin link ]
Giovanni Nigita
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Project Co-Developer
Giovanni Nigita
PhD student in Computer Science
Bioinformatics
Department of Mathematics and Computer Science
University of Catania, Italy [ Linkedin link ]
Name
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Member
Alessandro Laganà
Post-doc at Department of Molecular Virology, Immunology and Human Genetics
Comprehensive Cancer Center
The Ohio State University, Columbus OH, USA [ link ]
Name
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Member
Valentina Macca
Master Degree in Computer Science
Bioinformatics
Department of Mathematics and Computer Science
University of Catania, Italy [ Linkedin link ]
Name
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Project leader
Rosalba Giugno
Assistant Professor
Bioinformatics
Department of Clinical and Molecular Biomedicine
University of Catania, Italy [ Linkedin link ]
Alfredo Pulvirenti
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Project leader
Alfredo Pulvirenti
Assistant Professor
Bioinformatics
Department of Clinical and Molecular Biomedicine
University of Catania, Italy [ Linkedin link ]
Name
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Project leader
Alfredo Ferro
Full Professor
Bioinformatics
Department of Clinical and Molecular Biomedicine
University of Catania, Italy [ Linkedin link ]

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Input format

Use the following input file format:

> sequence_name | chr : start - end | strand:+/- |

i.e.

>sequence 1|17:7571720-7590863|-|

All input will be properly filtered by all characters that are not allowed.
Incorrectly formatted sequences will not be analyzed.

>Seq num 1|1:1252080-1252280|-|
>Seq num 2|y:550439-550998|+|
>Seq num 3|1:100360520-100360759|+|

Add new editing sites

Each new mismatch must have the following format:
absolute position ; chr ; assembly ; strand ; tissue ; organ ; pubmed resource

Use the following form to submit new editing sites (all input will be properly filtered):

Name or Institute
Your email address
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