Suffix trees and suffix arrays in primary and secondary storage by

In recent years the volume of string data has increased exponentially, and the speed at which these data is being generated has also increased. Some examples of string data includes biological sequences, internet webpages, and digitalized documents, to name a few. The indexing of biological sequence data is especially challenging due to the lack of natural word and sentence boundaries. Although many algorithms are able to deal with this lack of natural boundaries, they are not able to process the large quantity of data in reasonable time. To speed up the runtime of these algorithms, suffix trees and suffix arrays are routinely used to generate a set of starting positions quickly and/or narrow down the set of possibilities need to be considered. The first contribution of this dissertation is a linear time algorithm to sort all the suffixes of a string over a large alphabet of integers. The sorted order of suffixes of a string is also called suffix array, a data structure introduced by Manber and Myers that has numerous applications in pattern matching, string processing, and computational biology. Though the suffix tree of a string can be constructed in linear time and the sorted order of suffixes derived from it, a direct algorithm for suffix sorting is of great interest due to the space requirements of suffix trees. Our result is one of the first linear time suffix array construction algorithms, which improve upon the previously known O(n log n) time direct algorithms for suffix sorting. It can also be used to derive a different linear time construction algorithm for suffix trees. Apart from being simple and applicable for alphabets not necessarily of fixed size, this method of constructing suffix trees is more space efficient. The second contribution of this dissertation is providing a new suffix tree layout scheme for secondary storage and present construction, substring search, insertion and deletion algorithms