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An overview of the role of context-sensitive HMMs in the prediction of ncRNA genes

Yoon, Byung-Jun and Vaidyanathan, P. P. (2005) An overview of the role of context-sensitive HMMs in the prediction of ncRNA genes. In: IEEE/SP Workshop on Statistical Signal Processing,13th, Bordeaux, France, 17-20 July 2005. IEEE , Piscataway, NJ, pp. 1378-1383. ISBN 0780394038 http://resolver.caltech.edu/CaltechAUTHORS:YOOssp05

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Abstract

Non-coding RNAs (ncRNA) are RNA molecules that function in the cells without being translated into proteins. In recent years, much evidence has been found that ncRNAs play a crucial role in various biological processes. As a result, there has been an increasing interest in the prediction of ncRNA genes. Due to the conserved secondary structure in ncRNAs, there exist pairwise dependencies between distant bases. These dependencies cannot be effectively modeled using traditional HMMs, and we need a more complex model such as the context-sensitive HMM (csHMM). In this paper, we overview the role of csHMMs in the RNA secondary structure analysis and the prediction of ncRNA genes. It is demonstrated that the context-sensitive HMMs can serve as an efficient framework for these purposes.


Item Type:Book Section
Additional Information:© 2005 IEEE. Reprinted with Permission. Publication Date: 17-20 July 2005. Posted online: 2005-08-22. Work supported in parts by the NSF grant CCF-0428326 and the Microsoft Research Graduate Fellowship.
Subject Keywords:biological techniques; encoding; genetic engineering; hidden Markov models; macromolecules; organic compounds; context-sensitive HMMS; ncRNA genes; noncoding RNA genes; secondary structure analysis
Record Number:CaltechAUTHORS:YOOssp05
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:YOOssp05
Alternative URL:http://dx.doi.org/10.1109/SSP.2005.1628811
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9734
Collection:CaltechAUTHORS
Deposited By: Kristin Buxton
Deposited On:12 Mar 2008
Last Modified:26 Dec 2012 09:52

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