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Simple alignment constraints for efficient alignment of RNA sequences using family-specific models

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1 Author(s)
Byung-Jun Yoon ; Dept. of Electrical & Computer Engineering, Texas A&M University, Collge Station, 77843-3128, USA

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.

Published in:

2009 IEEE International Workshop on Genomic Signal Processing and Statistics

Date of Conference:

17-21 May 2009