Exact matching of RNA secondary structure patterns

Exact matching of RNA secondary structure patterns

Many RNA structures are assembled from a collection of RNA motifs, which appear repeatedly and in various combinations. Identification of RNA structural motifs will enhance our understanding of RNA structures and functions. Searching for secondary structural patterns in sequence databases is the basic technique and fundamental problem for extracting and identifying such motifs. A number of algo...

Exact Pattern Matching for RNA Secondary Structures

Exact Pattern Matching for RNA Structure Ensembles

ExpaRNA’s core algorithm computes, for two fixed RNA structures, a maximal non-overlapping set of maximal exact matchings. We introduce an algorithm ExpaRNA-P that solves the lifted problem of finding such sets of exact matchings in entire Boltzmann-distributed structure ensembles of two RNAs. Due to a novel kind of structural sparsification, the new algorithm maintains the time and space compl...

Algorithms for pattern matching and discovery in RNA secondary structure

Text-indexing structures provide significant advantages in the solution of many problems related to string analysis and comparison, and are nowadays widely used in the analysis of biological sequences. In this paper, we present some applications of affix trees to problems of exact and approximate pattern matching and discovery in RNA sequences. By allowing bidirectional search for symmetric pat...

Exact Folding Dynamics of RNA Secondary Structures

Barrier trees consisting of local minima and their connecting saddle points imply a natural coarse-graining for the description of the energy landscape of RNA secondary structures. Here we show that, based on this approach, it is possible to predict the folding behavior of RNA molecules by numerical integration. Comparison with stochastic folding simulations shows reasonable agreement of the re...