RNA editing is a post-transcriptional alteration of RNA sequences that is able to affect protein structure as well as RNA and protein expression. A-to-I (Adenosine-to-Inosine) RNA editing is the most frequent and common post-transcriptional modification in human, where adenosine (A) deamination produces its conversion into inosine (I), which in turn is interpreted by the translation and splicing machineries as guanosine (G).

AIRlINER is an algorithmic approach to the assessment of A-to-I RNA editing sites in non-repetitive regions. It determines the editing probability of an adenosine by analyzing its flanking region of 10 nucleotides. Such pattern is then combined with a similar model calculated from un-edited sequences, resulting in the estimation of an unbiased editing probability.


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Download

From this page you can download our datasets and regression models.

Editing Probabilities

Here you can download a text file, which contains the probability matrix of nucleotides around an editing site.

Download

Random Probabilities

Here you can download a text file, which contains the probability matrix of nucleotides around a random site.

Download

Sequence Training Set

Here you can download a text file containing the list of the sequences used to compute probability matrices.

Download

Model Training Set

Here you can download a text file containing the matrix we used to train our logistic regression model.

Download

Regression Model

Here you can download an rds file, which contains our logistic regression model. The file can be used by importing it into R.

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Help

Why?

RNA editing is a post-transcriptional alteration of RNA sequences that is able to affect protein structure as well as RNA and protein expression. A-to-I (Adenosine-to-Inosine) RNA editing is the most frequent and common post-transcriptional modification in human, where adenosine (A) deamination produces its conversion into inosine (I), which in turn is interpreted by the translation and splicing machineries as guanosine (G). The disruption of the editing machinery has been associated to various human diseases such as cancer or neurodegenerative diseases. This biological phenomenon is catalyzed by members of the Adenosine Deaminase Acting on RNA (ADAR) family of enzymes and occurs on dsRNA structures. Despite the enormous efforts made in the last decade, the real biological function underlying such a phenomenon, as well as ADAR’s substrate features, still remain unknown.

Usage

Using AIRlINER is extremely simple. First of all an user need to prepare their own mRNA sequences in FASTA or Multi-FASTA format , making sure that each sequence contains only A, C, U, G bases. In AIRlINER Homepage the user can upload his own files by using the appropriate box, or copy its content into a textbox. Therefore, by clicking on Launch Airliner the computation process starts. To check its status, an informative message will be shown in the top right corner of the page.

When the process finishes, for each sequence the user will be able to see a table listing the adenosine contained therein. For each adenosine, if the flanking region is wide enough (10 nt), the editing probability will be shown. Also, to allow the user a quickly identification of the site location, the flanking region is stated in the table.

The user can also save the results in text file by clicking the Download Results link. The resulting file will contain the same data shown in each sequence table. The special value NA (Not Available) is indicated for those adenosines whose flanking region is not wide enough.

References

If you are using this service in your own work, please cite by:

  • Nigita G, Alaimo S, Ferro A, Giugno R and Pulvirenti A (2015). Knowledge in the Investigation of A-to-I RNA editing signals. Front. Bioeng. Biotechnol. 3:18. doi: 10.3389/fbioe.2015.00018

Contacts

For bugs reporting, please send an email to: alaimos@dmi.unict.it

Authors

G. Nigita
Dept. of Molecular Virology, Immunology and Medical Genetics
The Ohio State University
nigita@dmi.unict.it
S. Alaimo
Dept. of Mathematics and Computer Science
University of Catania
alaimos@dmi.unict.it
A. Ferro
Dept. of Clinical and Molecular Biomedicine
University of Catania
ferro@dmi.unict.it
R. Giugno
Dept. of Clinical and Molecular Biomedicine
University of Catania
giugno@dmi.unict.it
A. Pulvirenti
Dept. of Clinical and Molecular Biomedicine
University of Catania
apulvirenti@dmi.unict.it