Fast Search of Sequences with Complex Symbol Correlations using Profile Context-Sensitive HMMS and Pre-Screening Filters

14 years 6 months ago

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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 eig...

Byung-Jun Yoon, P. P. Vaidyanathan

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