ABSTRACT
Fundamental string data structures, and their myriad applications in computational molecular biology are the focus of this part of the handbook. Sequence alignments and string data structures form the twin foundations for many applications in computational genomics. The utility of string data structures stems from the fact that at a basic level, various types of DNA and RNA sequences, and protein sequences can be modeled as strings — DNA as strings over the alphabet {A,C,G,T}, RNA as strings over the alphabet {A,C,G,U}, and proteins as strings over an alphabet of size 20 corresponding to the 20 amino acid residues. While simplistic, modeling of biological sequences as mere strings serves as a sufficient level of abstraction for a plethora of applications.
