Displaying similar documents to “Computing evolutionary chains in musical sequences.”

Dynamic programming for reduced NFAs for approximate string and sequence matching

Jan Holub (2002)

Kybernetika

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searching for all occurrences of a pattern (string or sequence) in some text, where the pattern can occur with some limited number of errors given by edit distance. Several methods were designed for the approximate string matching that simulate nondeterministic finite automata (NFA) constructed for this problem. This paper presents reduced NFAs for the approximate string matching usable in case, when we are interested only in occurrences having edit distance less than or equal to a given...

A new practical linear space algorithm for the longest common subsequence problem

Heiko Goeman, Michael Clausen (2002)

Kybernetika

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This paper deals with a new practical method for solving the longest common subsequence (LCS) problem. Given two strings of lengths m and n , n ≥ m , on an alphabet of size s , we first present an algorithm which determines the length p of an LCS in O ( n s + min { m p , p ( n - p ) } ) time and O ( n s ) space. This result has been achieved before [ric94,ric95], but our algorithm is significantly faster than previous methods. We also provide a second algorithm which generates an LCS in O ( n s + min { m p , m log m + p ( n - p ) } ) time while preserving the linear space bound,...

A sparse dynamic programming algorithm for alignment with non-overlapping inversions

Alair Pereira Do Lago, Ilya Muchnik, Casimir Kulikowski (2005)

RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications

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Alignment of sequences is widely used for biological sequence comparisons, and only biological events like mutations, insertions and deletions are considered. Other biological events like inversions are not automatically detected by the usual alignment algorithms, thus some alternative approaches have been tried in order to include inversions or other kinds of rearrangements. Despite many important results in the last decade, the complexity of the problem of alignment with inversions...

Reservation table scheduling: branch-and-bound based optimization . integer linear programming techniques

Hadda Cherroun, Alain Darte, Paul Feautrier (2007)

RAIRO - Operations Research

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The recourse to operation research solutions has strongly increased the performances of scheduling task in the High-Level Synthesis (called hardware compilation). Scheduling a whole program is not possible as too many constraints and objectives interact. We decompose high-level scheduling in three steps. Step 1: Coarse-grain scheduling tries to exploit parallelism and locality of the whole program (in particular in loops, possibly imperfectly nested) with a rough view of the target...

Tuning the Zhu-Takaoka string matching algorithm and experimental results

Thomas Berry, Somasundaram Ravindran (2002)

Kybernetika

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In this paper we present experimental results for string matching algorithms which have a competitive theoretical worst case run time complexity. Of these algorithms a few are already famous for their speed in practice, such as the Boyer–Moore and its derivatives. We chose to evaluate the algorithms by counting the number of comparisons made and by timing how long they took to complete a given search. Using the experimental results we were able to introduce a new string matching algorithm...