Algorithms for biological sequence data

Sequences are a crucial concept in the bioinformatics field, as they can represent different kinds of biological data. Apart from the common string representations of DNA and protein sequences, many other kinds of biological data have an inherent sequential order. Thus, algorithms for representing, comparing, exploring, and analyzing biological sequences are numerous and diverse. In this thesis I explore two main kinds of biological sequences - those obtained from optical mapping images, and those from three-dimensional protein structures. The sequence representation allows for adapting and reusing algorithms across these quite distinct fields.