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RNAbor: a web server for RNA structural neighbors
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
2007 (English)In: Nucleic Acids Research, ISSN 0305-1048, Vol. 35, no Suppl. S: Web Server issue, W305-W309 p.Article in journal (Refereed) Published
Abstract [en]

RNAbor provides a new tool for researchers in the biological and related sciences to explore important aspects of RNA secondary structure and folding pathways. RNAbor computes statistics concerning delta-neighbors of a given input RNA sequence and structure (the structure can, for example, be the minimum free energy (MFE) structure). A delta-neighbor is a structure that differs from the input structure by exactly delta base pairs, that is, it can be obtained from the input structure by adding and/or removing exactly d base pairs. For each distance delta RNAbor computes the density of delta-neighbors, the number of delta-neighbors, and the MFE structure, or MFEd structure, among all delta-neighbors. RNAbor can be used to study possible folding pathways, to determine alternate low-energy structures, to predict potential nucleation sites and to explore structural neighbors of an intermediate, biologically active structure. The web server is available at http://bioinformatics.bc.edu/clotelab/RNAbor.

Place, publisher, year, edition, pages
2007. Vol. 35, no Suppl. S: Web Server issue, W305-W309 p.
Keyword [en]
Cluster Analysis, Computational Biology/*methods, Computer Simulation, Conserved Sequence, Databases, Genetic, Internet, Molecular Sequence Data, Nucleic Acid Conformation, RNA/*chemistry, RNA, Untranslated, Regulatory Sequences, Ribonucleic Acid, Sequence Alignment, Sequence Analysis, RNA, Sequence Homology, Nucleic Acid
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-96426DOI: 10.1093/nar/gkm255ISI: 000255311500057PubMedID: 17526527OAI: oai:DiVA.org:uu-96426DiVA: diva2:170995
Available from: 2007-11-13 Created: 2007-11-13 Last updated: 2010-02-19Bibliographically 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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