Function Annotation for Pseudoknot Using Structure Similarity

Authors:
Qingfeng Chen;Yi-Ping Phoebe Chen
Affiliations:
Guangxi University, Nanning and La Trobe University, Melbourne;La Trobe University, Melbourne
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2011

Citing 6
Cited 0

Computing the minimum Hausdorff distance between two point sets on a line under translation

Information Processing Letters
Fast subsequence matching in time-series databases

SIGMOD '94 Proceedings of the 1994 ACM SIGMOD international conference on Management of data
Efficient Time Series Matching by Wavelets

ICDE '99 Proceedings of the 15th International Conference on Data Engineering
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots

Bioinformatics
Searching Genomes for Noncoding RNA Using FastR

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Classification of ncRNAs using position and size information in deep sequencing data

Bioinformatics

Quantified Score

Hi-index	0.00

Visualization

Abstract

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.