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Flexible pattern matching in strings - practical on-line search algorithms for texts and biological sequences

This book presents a practical approach to string matching problems, focusing on the algorithms and implementations that perform best in practice, and includes all of the most significant new developments in complex pattern searching.
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Fast and flexible string matching by combining bit-parallelism and suffix automata

A new automaton to recognize suffixes of patterns with classes of characters is introduced, which seems very adequate for computational biology applications, since it is the fastest algorithm to search on DNA sequences and flexible searching is an important problem in that area.
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Factor Oracle: A New Structure for Pattern Matching

We introduce a new automaton on a word p, sequence of letters taken in an alphabet ?, that we call factor oracle. This automaton is acyclic, recognizes at least the factors of p, has m+1 states and a…
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A Bit-Parallel Approach to Suffix Automata: Fast Extended String Matching

A new algorithm for string matching called BNDM, which is the bit-parallel simulation of a known (but recent) algorithm called BDM, and which can be extended to handle classes of characters in the pattern and in the text, multiple patterns and to allow errors in thepattern or in thetext, combining simplicity, efficiency and flexibility.
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The Algorithmic of Gene Teams

This paper presents two algorithms for identifying gene teams formed by n genes placed on m linear chromosomes, which run in O(m2n2) time, and follows a direct and simple approach and a more tricky one, which requires linear space.
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Fast and Simple Character Classes and Bounded Gaps Pattern Matching, with Applications to Protein Searching

Two new practical CBG matching algorithms that are much simpler and faster than all the RE search techniques are designed, and a criterion based on the form of the CBG to choose a priori the fastest between both are proposed.
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Computing Common Intervals of K Permutations, with Applications to Modular Decomposition of Graphs

A new way to compute common intervals of K permutations based on a very simple and general notion of generators of common intervals, that can contain a quadratic number of intervals, as well as a linear space basis of this set of common interval.
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Composite Repetition-Aware Data Structures

Two data structures are described whose size depends on multiple measures of repetition at once, and that provide competitive tradeoffs between the time for counting and reporting all the exact occurrences of a pattern, and the space taken by the structure.
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Efficient Experimental String Matching by Weak Factor Recognition

A new notion of weak factor recognition that is the foundation of new data structures and on-line string matching algorithms, and a new automaton built on a string p = p1p2 ... pm that acts like an oracle on the set of factors pi ... pj.
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A General Practical Approach to Pattern Matching over Ziv-Lempel Compressed Text

A general technique for string matching when the text comes as a sequence of blocks is developed, which abstracts the essential features of Ziv-Lempel compression and presents the first algorithm to find all the matches of a pattern in a text compressed using LZ77.
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