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Title
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.
Authors
Eddy, Sean R
Abstract
Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs.