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

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

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Abstrakt

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.

OriginalsprogEngelsk
TitelAlgorithms in Bioinformatics : 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings
RedaktørerAaron Darling, Jens Stoye
Antal sider13
ForlagSpringer Publishing Company
Publikationsdato2013
Sider112-125
ISBN (Trykt)9783642404528
DOI
StatusUdgivet - 2013
Udgivet eksterntJa
Begivenhed13th International Workshop, WABI 2013 - Sophia Antipolis, Frankrig
Varighed: 2. sep. 20134. sep. 2013

Konference

Konference13th International Workshop, WABI 2013
LandFrankrig
By Sophia Antipolis
Periode02/09/201304/09/2013
NavnLecture Notes in Computer Science
Vol/bind8126
ISSN0302-9743

Bibliografisk note

The WABI proceedings will be published in the Lecture Notes in Computer Science: Lecture Notes in Bioinformatics series by Springer-Verlag.

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