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Fast search of sequences with complex symbol correlations using profile context-sensitive HMMS and pre-screening filters

Yoon, Byung-Jun and Vaidyanathan, P. P. (2007) Fast search of sequences with complex symbol correlations using profile context-sensitive HMMS and pre-screening filters. In: IEEE International Conference on Acoustics, Speech and Signal Processing, 2007 (ICASSP 2007), Honolulu, HI, 15-20 April 2007. Vol.1. IEEE , Piscataway, NJ, I-345-I-348. ISBN 1424407281.

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Recently, profile context-sensitive HMMs (profile-csHMMs) have been proposed which are very effective in modeling the common patterns and motifs in related symbol sequences. Profile-csHMMs are capable of representing long-range correlations between distant symbols, even when these correlations are entangled in a complicated manner. This makes profile-csHMMs an useful tool in computational biology, especially in modeling noncoding RNAs (ncRNAs) and finding new ncRNA genes. However, a profile-csHMM based search is quite slow, hence not practical for searching a large database. In this paper, we propose a practical scheme for making the search speed significantly faster without any degradation in the prediction accuracy. The proposed method utilizes a pre-screening filter based on a profile-HMM, which filters out most sequences that will not be predicted as a match by the original profile-csHMM. Experimental results show that the proposed approach can make the search speed eighty times faster.

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Vaidyanathan, P. P.0000-0003-3003-7042
Additional Information:© 2007 IEEE. Reprinted with Permission. Publication Date: 15-20 April 2007. Posted online: 2007-06-04. Work supported in parts by the NSF grant CCF-0636799 and the Microsoft Research Graduate Fellowship.
Subject Keywords:homology search; profile-csHMM; pseudoknot; noncoding RNA (ncRNA); context-sensitve HMM (csHMM)
Record Number:CaltechAUTHORS:YOOicassp07b
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9710
Deposited By: Kristin Buxton
Deposited On:10 Mar 2008
Last Modified:08 Nov 2021 21:01

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