Efficient RNA structure comparison algorithms.

Recently proposed relative addressing-based ([Formula: see text]) RNA secondary structure representation has important features by which an RNA structure database can be stored into a suffix array. A fast substructure search algorithm has been proposed based on binary search on this suffix array. Using this substructure search algorithm, we present a fast algorithm that finds the largest common substructure of given multiple RNA structures in [Formula: see text] format.

PMBC: pattern mining from biological sequences with wildcard constraints.

Patterns/subsequences frequently appearing in sequences provide essential knowledge for domain experts, such as molecular biologists, to discover rules or patterns hidden behind the data. Due to the inherent complex nature of the biological data, patterns rarely exactly reproduce and repeat themselves, but rather appear with a slightly different form in each of its appearances. A gap constraint (In this paper, a gap constraint (also referred to as a wildcard) is a character that can be substituted for any character predefined in an alphabet.

A space-efficient algorithm for the constrained pairwise sequence alignment problem.

The constrained pairwise sequence alignment (CPSA) problem aims to align two given sequences by aligning their similar subsequences in the same region under the guidance of a given pattern (constraint). Let the lengths of the sequences be m, and n where n View Article and Find Full Text PDF