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Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.
Ryan R Rahrig1, Neocles B Leontis, Craig L Zirbel
1Department of Mathematics and Statistics at Ohio Northern University, Ada, OH 45810, USA. r-rahrig@onu.edu
Bioinformatics (Oxford, England)
|October 9, 2010
Summary
Accurate alignment of large homologous RNA 3D structures is crucial for understanding variability. R3D Align offers a novel nucleotide-by-nucleotide algorithm and web server, achieving superior accuracy in RNA structure comparison.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Comparing 3D structures of homologous RNA molecules reveals sequence and structural variability.
- Accurate automated tools are essential for comparing large RNA 3D structures.
- RNA flexibility necessitates specialized algorithms for precise structural alignment.
Purpose of the Study:
- Introduce a new algorithm and web server for aligning large homologous RNA 3D structures.
- Enable nucleotide-by-nucleotide alignment using local superpositions.
- Merge local alignments into a global alignment via a maximum clique algorithm.
Main Methods:
- Developed a novel algorithm implemented in the R3D Align program suite and web server.
- Utilized local superpositions to accommodate RNA flexibility.
- Employed a maximum clique algorithm on a 'local alignment' graph for global alignment.
Main Results:
- R3D Align demonstrated superior accuracy compared to state-of-the-art methods and hand-crafted alignments for 5S, 16S, and 23S rRNA.
- Evaluated alignment accuracy using the number of aligned base pairs and geometric similarity measures.
- Introduced new diagnostic tools for structural evaluation of RNA alignments within the R3D Align suite.
Conclusions:
- R3D Align provides highly accurate alignments for large homologous RNA 3D structures.
- The algorithm effectively handles RNA flexibility and integrates local alignments into a global comparison.
- R3D Align is freely available as a web server and downloadable MATLAB source code.
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