SIMPLE ALIGNMENT CONSTRAINTS FOR EFFICIENT ALIGNMENT OF RNA SEQUENCES USING FAMILY-SPECIFIC MODELS Conference Paper uri icon

abstract

  • 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.

author list (cited authors)

  • Yoon, B.

citation count

  • 0

publication date

  • May 2009

publisher