MOTIVATION Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be...

We present a string-matching program that runs on the GPU. Our program, Cmatch, achieves a speedup of as much as 35x on a recent GPU over the equivalent CPU-bound version. String matching has a long history in computational biology with roots in finding similar proteins and gene sequences in a database of known sequences. The explosion in sequence data available in the 80s and 90s motivated the...

As sequenced genomes become larger and sequencing process becomes faster, there is a need to develop a tool to analyze sequences in the whole genomic scale. However, on-memory algorithms such as suffix tree and suffix array are not applicable to the analysis of whole genome sequence set, since the size of individual whole genome ranges from several million base pairs to hundreds billion base pa...

Suffix Tree Clustering (STC) uses the suffix tree structure to find a set of snippets that share a common phrase and uses this information to propose clusters. As a result, STC is a fast incremental algorithm for automatic clustering and labeling but it cannot cluster semantically similar snippets. However, the meaning of the words is indeed an important property that relates them to other word...

Protein structure analysis is one of the most important research issues in the post-genomic era, and faster and more accurate query data structures for such 3-D structures are highly desired for research on proteins. This paper proposes a new data structure for indexing protein 3-D structures. For strings, there are many efficient indexing structures such as suffix trees, but it has been consid...

1. Introduction Vowel harmony is a requirement by which vowels in a certain domain agree in one or more phonetic features. 1 In Hungarian, the feature subject to harmony is the horizontal position of the tongue ([±back]). In many Hungarian roots, vowels in a word are either all front or all back, as in öröm 'joy', város 'city' (umlaut denotes front round vowels, and acute accent denotes length)...

Index structures like the suffix tree or the suffix array are of utmost importance in stringology, most notably in exact string matching. In the last decade, research on compressed index structures has flourished because the main problem in many applications is the space consumption of the index. It is possible to simulate the matching of a pattern against a suffix tree on an enhanced suffix ar...

A suffix tree (also called suffix trie, PAT tree or, position tree) is a powerful data structure that presents the suffixes of a given string in a way that allows a fast implementation of important string operations. The idea behind suffix trees is to assign to each symbol of a string an index corresponding to its position in the string. The first symbol in the string will have the index 1, the...

We present a new variant of the suffix tree called a distributed suffix tree (DST) which allows for much larger databases of strings to be handled efficiently. The method is based on a new linear time construction algorithm for subtrees of a suffix tree. The new data structure tackles the memory bottleneck problem by constructing these subtrees independently and in parallel. It is designed for ...

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii Chapter 1: Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 The Models of Computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.2 Our Contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...