Arc-annotated sequences are useful in representing the structural information of RNA
sequences. In general, RNA secondary and tertiary structures can be represented as a set of …

The aim of this book is to introduce the reader to some of the best techniques for data mining
in bioinformatics in the hope that the reader will build on them to make new discoveries on …

We show that calculating contact map overlap (a measure of similarity of protein structures)
is NP-hard, but can be solved in polynomial time for several interesting and relevant special …

Background The discovery of functional non-coding RNA sequences has led to an
increasing interest in algorithms related to RNA analysis. Traditional sequence alignment …

Molecular biologists use algorithms that compare and otherwise analyze sequences that
represent genetic and protein molecules. Most of these algorithms, however, operate on the …

Our study presents a novel method for analyzing biological sequences, utilizing Pairwise
Amino Acid Composition and Amino Acid physicochemical properties to construct a feature …

We study two new problems in sequence alignment both from a practical and a theoretical
view, using tools from combinatorial optimization to develop branch-and-cut algorithms. The …

We describe a theoretical unifying framework to express the comparison of RNA structures,
which we call alignment hierarchy. This framework relies on the definition of common …

Abstract The Longest Common Subsequence problem seeks a longest subsequence of
every member of a given set of strings. It has applications, among others, in data …

This paper examines the complexity of comparing sequences that have arcs linking symbol
pairs. Such arc-annotated sequences can represent molecular sequences with bonds …