## A Memory-Efficient Dynamic Programming Algorithm for Optimal Alignment of a Sequence to an RNA Secondary Structure (2002)

by
Sean R. Eddy

Citations: | 76 - 6 self |

### BibTeX

@MISC{Eddy02amemory-efficient,

author = {Sean R. Eddy},

title = {A Memory-Efficient Dynamic Programming Algorithm for Optimal Alignment of a Sequence to an RNA Secondary Structure},

year = {2002}

}

### Years of Citing Articles

### OpenURL

### Abstract

Background: 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. Results:...