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Automated prediction of three-way junction topological families in RNA secondary structures

Paper ID Volume ID Publish Year Pages File Format Full-Text
15178 1386 2012 5 PDF Available
Title
Automated prediction of three-way junction topological families in RNA secondary structures
Abstract

We present an algorithm for automatically predicting the topological family of any RNA three-way junction, given only the information from the secondary structure: the sequence and the Watson–Crick pairings. The parameters of the algorithm have been determined on a data set of 33 three-way junctions whose 3D conformation is known. We applied the algorithm on 53 other junctions and compared the predictions to the real shape of those junctions. We show that the correct answer is selected out of nine possible configurations 64% of the time. Additionally, these results are noticeably improved if homology information is used. The resulting software, Cartaj, is available online and downloadable (with source) at: http://cartaj.lri.fr.

Graphical abstractThe prediction workflow. A given RNA three-way junction can have three stackings; for each stacking, the junction can be in three families (A, B or C), depending on the angle of the third helix. This gives nine configurations. We compute a score for each configuration, and the configuration with the best score is our prediction. Figure optionsDownload full-size imageDownload as PowerPoint slideHighlights► We present an algorithm for automatically predicting the topological family of any RNA three-way junction, given only the information from the secondary structure. ► We show that the correct answer is selected out of nine possible con gurations 64% of the time. Additionally, these results are noticeably improved if homology information used. ► This work may have important applications in the field of three-dimensional modelling of RNA molecules. ► The resulting software, Cartaj, is available online and downloadable (with source) at: http://cartaj.lri.fr.

Keywords
RNA tertiary structure; Three-way junctions; Prediction
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Automated prediction of three-way junction topological families in RNA secondary structures
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 37, April 2012, Pages 1–5
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us