Suffix trees are the most frequently used data structures in algorithms on words. In this paper, we consider the depth of a compact suffix tree, also known as the PAT tree, under some simple probabilistic assumptions. For a biased memoryless source, we prove that the limiting distribution for the depth in a PAT tree is the same as the limiting distribution for the depth in a PATRICIA trie, even...

Vergleichende Genomanalyse ist ein relativ neues Gebiet der Bioinformatik, das durch die Verfügbarkeit einer immer größer werdender Zahl sequenzierter Genomen an Bedeutung gewinnt. Die vorliegende Dissertation präsentiert Algorithmen und Softwarewerkzeuge, mit denen mehrere Genome effizient verglichen werden können. Die vorgestellten Algorithmen lösen bisher offene Probleme der theoretischen Bi...

We present a new and simple algorithm to reconstruct suffix links in suffix trees and suffix arrays. The algorithm is based on observations regarding suffix tree construction algorithms. With our algorithm we bring suffix arrays even closer to the ease of use and implementation of suffix trees.

In this paper, a contrastive evaluation of massively parallel implementations of suffix tree and suffix array to accelerate genome sequence matching are proposed based on Intel Core i7 3770K quad-core and NVIDIA GeForce GTX680 GPU. Besides suffix array only held approximately 20%∼30% of the space relative to suffix tree, the coalesced binary search and tile optimization make suffix array clearl...

We consider suffix tree construction for situations with missing suffix links. Two examples of such situations are suffix trees for parameterized strings and suffix trees for two-dimensional arrays. These trees also have the property that the node degrees may be large. We add a new backpropagation component to McCreight’s algorithm and also give a high probability hashing scheme for large degre...

The thesis describes extensive studies on various algorithms for efficient string processing. Data available in/via computers are often of enormous size, and thus, it is significantly important and necessary to invent timeand space-efficient methods to process them. Most of such data are, in fact, stored and manipulated as strings. String matching is most fundamental in string processing, where...

Iowa State University 1.1 Basic Definitions and Properties . . . . . . . . . . . . . . . . . . . . 1-1 1.2 Linear Time Construction Algorithms . . . . . . . . . . . . . 1-4 Suffix Trees vs. Suffix Arrays • Linear Time Construction of Suffix Trees • Linear Time Construction of Suffix Arrays • Space Issues 1.3 Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...