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A New Method for the Similarity Analysis of RNA Secondary Structures

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A great challenge on the similarity analysis of RNA molecules is to infer common catalytic or regulatory functions based on primary sequences and secondary structures. So far, various methods for the similarity analysis have been developed. Almost all of them concentrated on analyzing their primary sequences or their structural units. In this paper, we take RNA secondary structures with pseudoknots into account and transform them into linear symbolic sequences in our new method. Furthermore, we analyze the similarity relationships among 20 species using LZ complexity. The results adequately indicate the validity of our new method.
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Keywords: LINEAR SYMBOLIC SEQUENCES; LZ COMPLEXITY; PSEUDOKNOTS; RNA SECONDARY STRUCTURES; SIMILARITY ANALYSIS

Document Type: Research Article

Publication date: November 1, 2011

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  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
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