In this paper, we adopt a representation of secondary structure called secondary expressions, and present two algorithms for finding all exact matches of a ...
[PDF] Exact Matching of RNA Secondary Structure Patterns - CiteSeerX
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These basic patterns appear repeatedly and in various combinations to form different RNA types and define their unique struc- tural and functional properties.
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The novel algorithm ExpaRNA-P computes exactly matching sequence-structure motifs in entire Boltzmann-distributed structure ensembles of two RNAs; thereby we ...
In this paper, we adopt a representation of sec- ondary structure called secondary expressions, and present two algorithms for finding all exact matches of a ...
In this article, we introduce a new RNA sequence–structure comparison method which maintains exact matching substructures. Existing common substructures are ...
Oct 22, 2024 · Many RNA structures are assembled from a collection of RNA motifs, which appear re-peatedly and in various combinations.
[PDF] Exact Pattern Matching for RNA Structure Ensembles - CiteSeerX
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It computes the sequence-structure- conserved elements that form highly probable local substructures in the RNA structure ensemble of both input RNAs; ...
ExpaRNA's core algorithm computes, for two fixed RNA structures, a maximal non-overlapping set of maximal exact matchings. We introduce an algorithm ...
Dec 1, 2023 · Pairwise alignment determines the best-matching pattern of two sequences, whereas multiple sequence alignment involves multiple sequences ...
Dec 29, 2014 · This paper considers pattern matching as well as local alignment between two RNA structures. For pattern matching, we present two algorithms, ...