Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures

Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Abstract

Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium therefore provides useful information on the overall shape of the molecule can provide insights into the interplay of its functional domains. Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between arbitrary nucleotides can be computed in polynomial time by means of dynamic programming. A naive implementation would yield recursions with a very high time complexity of O(n 11). Although we were able to reduce this to O(n 6) for many practical applications a further reduction seems difficult. We conclude, therefore, that sampling approaches, which are much easier to implement, are also theoretically favorable for most real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics : 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings
EditorsAaron Darling, Jens Stoye
Number of pages13
PublisherSpringer
Publication date2013
Pages112-125
ISBN (Print)9783642404528
DOIs
Publication statusPublished - 2013
Externally publishedYes
Event13th International Workshop, WABI 2013 - Sophia Antipolis, France
Duration: 2. Sept 20134. Sept 2013

Conference

Conference13th International Workshop, WABI 2013
Country/TerritoryFrance
City Sophia Antipolis
Period02/09/201304/09/2013
SeriesLecture Notes in Computer Science
Volume8126
ISSN0302-9743

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