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On topological indices for small RNA graphs

Paper ID Volume ID Publish Year Pages File Format Full-Text
15159 1383 2012 6 PDF Available
Title
On topological indices for small RNA graphs
Abstract

The secondary structure of RNAs can be represented by graphs at various resolutions. While it was shown that RNA secondary structures can be represented by coarse grain tree-graphs and meaningful topological indices can be used to distinguish between various structures, small RNAs are needed to be represented by full graphs. No meaningful topological index has yet been suggested for the analysis of such type of RNA graphs. Recalling that the second eigenvalue of the Laplacian matrix can be used to track topological changes in the case of coarse grain tree-graphs, it is plausible to assume that a topological index such as the Wiener index that represents all Laplacian eigenvalues may provide a similar guide for full graphs. However, by its original definition, the Wiener index was defined for acyclic graphs. Nevertheless, similarly to cyclic chemical graphs, small RNA graphs can be analyzed using elementary cuts, which enables the calculation of topological indices for small RNAs in an intuitive way. We show how to calculate a structural descriptor that is suitable for cyclic graphs, the Szeged index, for small RNA graphs by elementary cuts. We discuss potential uses of such a procedure that considers all eigenvalues of the associated Laplacian matrices to quantify the topology of small RNA graphs.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► For small RNAs a coarse grain tree-graph representation may not suffice and a full graph representation is needed. ► Suggested topological indices for small RNA full graphs contain information from all Laplacian eigenvalues. ► Elementary cuts can be used to calculate topological indices for small RNA full graphs in an intuitive way.

Keywords
RNA secondary structure; RNA graph representation; Laplacian eigenvalues; Small RNA graphs
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On topological indices for small RNA graphs
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 41, December 2012, Pages 35–40
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