Introduction

String search, edit, and alignment tools have been extensively used in studies of molecular evolution. However, their use has primarily been aimed at comparing strings representing single genes or single proteins. For example, evolutionary studies have usually selected a single protein and have examined how the amino acid sequence for that protein differs in different species. Accordingly, string edit and alignment algorithms have been guided by objective functions that model the most common types of mutations occurring at the level of a single gene or protein: point mutations or amino acid substitutions, single character insertions and deletions, and block insertions and deletions (gaps).

Recently, attention has been given to mutations that occur on a scale much larger than the single gene. These mutations occur at the chromosome or at the genome level and are central in the evolution of the whole genome. These larger-scale mutations have features that can be quite different from gene- or protein-level mutations. With more genome-level molecular data becoming available, larger-scale string comparisons may give insights into evolution that are not seen at the single gene or protein level.

The guiding force behind genome evolution is “duplication with modification” [126, 128, 301, 468]. That is, parts of the genome are duplicated, possibly very far away from the original site, and then modified. Other genome-level mutations of importance include inversions, where a segment of DNA is reversed; translocations, where the ends of two chromosomes (telomeres) are exchanged; and transpositions, where two adjacent segments of DNA exchange places.