Motivation: The relative ease and low cost of current generation sequencing technologies
has led to a dramatic increase in the number of sequenced genomes for species across the …

This handbook provides an up-to-date compendium of fundamental computer science
topics, techniques, and applications. Along with updating and revising many of the existing …

Molecular biology is becoming a computationally intense realm of contemporary science
and faces some of the current grand scientific challenges. In its context, tools that identify …

String searching is a subject of both theoretical and practical interest in computer science.
This book presents a bibliographic overview of the field and an anthology of detailed …

This paper focuses on space efficient representations of rooted trees that permit basic
navigation in constant time. While most of the previous work has focused on binary trees, we …

The enormous complexity of biological systems at the molecular level must be answered
with powerful computational methods. Computational biology is a young field, but has seen …

Motivation: To allow a direct comparison of the genomic DNA sequences of sufficiently
similar organisms, there is an urgent need for software tools that can align more than two …

We revisit the classic combinatorial pattern matching problem of finding a longest common
subsequence (LCS). For strings x and y of length n, a textbook algorithm solves LCS in time …

Widely used evaluation metrics for text generation either do not work well with longer texts or
fail to evaluate all aspects of text quality. In this paper, we introduce a new metric called …

The string editing problem for input strings x and y consists of transforming x into y by
performing a series of weighted edit operations on x of overall minimum cost. An edit …