The Human Genome Project.

A simple fast hybrid pattern-matching algorithm

The aim of this survey is to provide insight into the sequential algorithms that have been proposed to compute exact "regularities" in strings; that is, covers (or quasiperiods), seeds, repetitions, runs (or maximal periodicities), and repeats. After outlining and evaluating the algorithms that have been proposed for their computation, I suggest possibly productive future directions of research.

/pdf/computing-regularities-in-strings-4z5veqfogs.pdf

Computing regularities in strings

In this paper, we consider the pattern matching problem in DNA and RNA sequences where either the pattern or the text can be degenerate, i.e., contain sets of characters. We present an asymptotically faster algorithm for the above problem that works in O(n log m) time, where n and m is the length of the text and the pattern respectively. We also suggest an efficient implementation of our algorithm, which works in linear time when the pattern size is small. Finally, we also describe how our approach can be used to solve the distributed pattern matching problem.

A New Approach to Pattern Matching in Degenerate DNA/RNA Sequences and Distributed Pattern Matching

We describe a hybrid pattern-matching algorithm that works on both regular and indeterminate strings. This algorithm is inspired by the recently proposed hybrid algorithm FJS [11] and its indeterminate successor [15]. However, as discussed in this paper, because of the special properties of indeterminate strings, it is not straightforward to directly migrate FJS to an indeterminate version. Our new algorithm combines two fast pattern-matching algorithms, Shift-And and BMS (the Sunday variant of the Boyer-Moore algorithm), and is highly adaptive to the nature of the text being processed. It avoids using the border array, therefore avoids some of the cases that are awkward for indeterminate strings. Although not always the fastest in individual test cases, our new algorithm is superior in overall performance to its two component algorithms — perhaps a general advantage of hybrid algorithms.

An adaptive hybrid pattern-matching algorithm on indeterminate strings

Fast pattern-matching on indeterminate strings

http://www.cas.mcmaster.ca/~bill/best/periodicity/09Indeterminate.pdf

A new approach to the periodicity lemma on strings with holes

Indeterminate strings, prefix arrays & undirected graphs

We describe a hybrid pattern-matching algorithm that works on both regular and indeterminate strings. This algorithm is inspired by the recently proposed hybrid algorithm FJS and its indeterminate successor. However, as discussed in this paper, because of the special properties of indeterminate strings, it is not straightforward to directly migrate FJS to an indeterminate version. Our new algorithm combines two fast pattern-matching algorithms, ShiftAnd and BMS (the Sunday variant of the Boyer-Moore algorithm), and is highly adaptive to the nature of the text being processed. It avoids using the border array, therefore avoids some of the cases that are awkward for indeterminate strings. Although not always the fastest in individual test cases, our new algorithm is superior in overall performance to its two component algorithms — perhaps a general advantage of hybrid algorithms.

/pdf/an-adaptive-hybrid-pattern-matching-algorithm-on-3ajborzoah.pdf

Shu Wang

Papers

Fast pattern-matching on indeterminate strings

An adaptive hybrid pattern-matching algorithm on indeterminate strings

A new approach to the periodicity lemma on strings with holes

Indeterminate strings, prefix arrays & undirected graphs

An adaptive hybrid pattern-matching algorithm on indeterminate strings