The affix array data structure and its applications to RNA secondary structure analysis

Abstract

Efficient string-processing in large data sets like complete genomes is strongly connected to the suffix tree and similar index data structures. With respect to complex structural string analysis like the search for RNA secondary structure patterns, unidirectional suffix tree algorithms are inferior to bidirectional algorithms based on the affix tree data structure. The affix tree incorporates the suffix tree and the suffix tree of the reverse text in one tree structure but suffers from its large memory requirements. In this paper I present a new data structure, denoted affix array, which is equivalent to the affix tree with respect to its algorithmic functionality, but with smaller memory requirements and improved performance. I will show a linear time construction of the affix array without making use of the linear time construction of the affix tree. I will also show how bidirectional affix tree traversals can be transferred to the affix array and present the impressive results of large scale RNA secondary structure analysis based on the new data structure.