Titlebook: Combinatorial Pattern Matching; 16th Annual Symposiu Alberto Apostolico,Maxime Crochemore,Kunsoo Park Conference proceedings 2005 Springer-

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Lecture Notes in Electrical Engineeringdescribed in [5] yields an .(. .) result for spliced alignment, regardless of filtration mode..In this paper we suggest a new algorithm which targets the case where filtering has been applied to the data, resulting in a set of .(.) candidate exon blocks. Our algorithm yields an . solution for this case.

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Sharper Upper and Lower Bounds for an Approximation Scheme for , ,problem is an abstraction of motif finding, a common bioinformatics discovery task. The PTAS due to Li . is simple, and a preliminary implementation [8] gave reasonable results in practice. However, the previously known bounds on its performance are useless when runtimes are actually manageable. Her

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Succinct Suffix Arrays Based on Run-Length Encoding,d text), permits efficient search for the occurrences of a pattern .=. . . .... . . in ., and is able to reproduce any text substring, so the self-index replaces the text. Several remarkable self-indexes have been developed in recent years. They usually take .(. .) or .(. .) bits, being . . the .th

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Linear-Time Construction of Compressed Suffix Arrays Using ,(, log ,)-Bit Working Space for Large Aor constructing these index data structures have been developed. Recently, Hon et al. [11] proposed a construction algorithm using .(. ·loglog|Σ|) time and .(.log|Σ|)-bit working space, which is the fastest algorithm using .(.log|Σ|)-bit working space..In this paper we give an efficient algorithm to

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Faster Algorithms for ,,,-Matching and Related Problems,ms is shown to be .(. log .), where . is the pattern length, . is the text length and . a given integer. Our approach makes use of Fourier transform methods and the running times are independent of the alphabet size. . algorithms for the .-matching and total-difference problems are also given. In al

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A Fast Algorithm for Approximate String Matching on Gene Sequences,ations including text processing and DNA sequence analysis. In this paper, we present a fast algorithm for approximate string matching, called FAAST. It aims at solving a popular variant of the approximate string matching problem, the ., whose objective is to find all occurrences of a short pattern