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Boltzmann probability of RNA structural neighbors and riboswitch detection
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
2007 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 23, no 16, 2054-2062 p.Article in journal (Refereed) Published
Abstract [en]

Motivation: We describe algorithms implemented in a new software package, RNAbor, to investigate structures in a neighborhood of an input secondary structure of an RNA sequence s. The input structure could be the minimum free energy structure, the secondary structure obtained by analysis of the X-ray structure or by comparative sequence analysis, or an arbitrary intermediate structure.

Results: A secondary structure of s is called a -neighbor of if and differ by exactly base pairs. RNAbor computes the number (N), the Boltzmann partition function (Z) and the minimum free energy (MFE) and corresponding structure over the collection of all -neighbors of . This computation is done simultaneously for all m, in run time O (mn3) and memory O(mn2), where n is the sequence length. We apply RNAbor for the detection of possible RNA conformational switches, and compare RNAbor with the switch detection method paRNAss. We also provide examples of how RNAbor can at times improve the accuracy of secondary structure prediction.

Place, publisher, year, edition, pages
2007. Vol. 23, no 16, 2054-2062 p.
National Category
Biological Sciences Computer and Information Science
URN: urn:nbn:se:uu:diva-96425DOI: 10.1093/bioinformatics/btm314ISI: 000249818300004OAI: oai:DiVA.org:uu-96425DiVA: diva2:170994
Available from: 2007-11-13 Created: 2007-11-13 Last updated: 2011-01-25Bibliographically approved
In thesis
1. A Study in RNA Bioinformatics: Identification, Prediction and Analysis
Open this publication in new window or tab >>A Study in RNA Bioinformatics: Identification, Prediction and Analysis
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Research in the last few decades has revealed the great capacity of the RNA molecule. RNA, which previously was assumed to play a main role only as an intermediate in the translation of genes to proteins, is today known to play many important roles in the cell in addition to that as a messenger RNA and transfer RNA, including the ability to catalyze reactions and gene regulations at various levels.

This thesis investigates several computational aspects of RNA. We will discuss identification of novel RNAs and RNAs that are known to exist in related species, RNA secondary structure prediction, as well as more general tools for analyzing, visualizing and classifying RNA sequences.

We present two benchmark studies concerning RNA identification, both de novo identification/characterization of single RNA sequences and homology search methods.

We develope a novel algorithm for analysis of the RNA folding landscape that is based on the nearest neighbor energy model adopted in many secondary structure prediction programs. We implement this algorithm, which computes structural neighbors of a given RNA secondary structure, in the program RNAbor, which is accessible on a web server.

Furthermore, we combine a mutual information based structure prediction algorithm with a sequence logo visualization to create a novel visualization tool for analyzing an RNA alignment and identifying covarying sites.

Finally, we present extensions to sequence logos for the purpose of tRNA identity analysis. We introduce function logos, which display features that distinguish functional subclasses within a large set of structurally related sequences, as well as the inverse logos, which display underrepresented features. For the purpose of comparing tRNA identity elements between different taxa we introduce two contrasting logos, the information difference and the Kullback-Leibler divergence difference logos.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 75 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 364
RNA, bioinformatics, secondary structure, structure prediction, dynamic programming, energy landscape, homology search, sequence logo, tRNA
National Category
Bioinformatics (Computational Biology)
urn:nbn:se:uu:diva-8305 (URN)978-91-554-7019-7 (ISBN)
Public defence
2007-12-07, B42, BMC, Husargatan 3, Uppsala, 13:00
Available from: 2007-11-13 Created: 2007-11-13Bibliographically approved

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