SIMPLE ALIGNMENT CONSTRAINTS FOR EFFICIENT ALIGNMENT OF RNA SEQUENCES USING FAMILY-SPECIFIC MODELS
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In this extended abstract, we present a simple method for finding alignment constraints that can be used for efficient alignment of RNAs based on family-specific models, such as profile context-sensitive HMMs (profile-csHMMs) and covariance models (CMs). The alignment constraints are established based on the alignment positions predicted by a profile-HMM. Application of the proposed constraints to the profile-csHMM based structural RNA alignment method significantly improved the average alignment speed without degrading the alignment accuracy.
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