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Issue No. 06 - November/December (2011 vol. 8)
ISSN: 1545-5963
pp: 1535-1544
Qingfeng Chen , Guangxi University, Nanning and La Trobe University, Melbourne
Yi-Ping Phoebe Chen , La Trobe University, Melbourne
Many raw biological sequence data have been generated by the human genome project and related efforts. The understanding of structural information encoded by biological sequences is important to acquire knowledge of their biochemical functions but remains a fundamental challenge. Recent interest in RNA regulation has resulted in a rapid growth of deposited RNA secondary structures in varied databases. However, a functional classification and characterization of the RNA structure have only been partially addressed. This article aims to introduce a novel interval-based distance metric for structure-based RNA function assignment. The characterization of RNA structures relies on distance vectors learned from a collection of predicted structures. The distance measure considers the intersected, disjoint, and inclusion between intervals. A set of RNA pseudoknotted structures with known function are applied and the function of the query structure is determined by measuring structure similarity. This not only offers sequence distance criteria to measure the similarity of secondary structures but also aids the functional classification of RNA structures with pesudoknots.
Pseudoknot, function, stem, loop, similarity, distance, structure.

Y. Phoebe Chen and Q. Chen, "Function Annotation for Pseudoknot Using Structure Similarity," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. , pp. 1535-1544, 2011.
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