Efficient pattern matching for RNA secondary structures

Exact Pattern Matching for RNA Secondary Structures

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...

Prediction and pattern matching algorithms for RNA multi-structures

RNA (ribonucleic acid) molecules have various functions in cells. Just as they can store anddeliver the DNA message for the protein synthesis (messenger RNAs), they can also directly cat-alyze chemical reactions or act as a regulator (functional RNAs, also called non-coding RNAs).Nowadays, recent sequencing technologies yield billions of genomic sequences – DNA, RNA– at a very s...

Pattern Matching and Local Alignment for RNA Structures

The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A,C,G,U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between A − U and G − C. For secondary structures, these bonds have been traditionally assumed to be one-to-one and non-crossing. This paper considers pattern matching...

Memory Efficient Folding Algorithms for Circular RNA Secondary Structures

BACKGROUND A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from 'internal' and 'external' substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package whi...