Natsuhiko Futamura

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We present practical parallel algorithms using prefix computations for various problems that arise in pairwise comparison of biological sequences. We consider both constant and affine gap penalty functions, full-sequence and subsequence matching, and space-saving algorithms. The best known sequential algorithms solve these problems in Omn time and Om + n(More)
We present a parallel algorithm for lexicographi-cally sorting the suffixes of a string. Suffix sorting has applications in string processing, data compression and computational biology. The ordered list of suffixes of a string stored in an array is known as Suffix Array, an important data structure in string processing and computational biology. Our focus(More)
One of the central issues in router performance is IP address lookup based on longest prefix matching. IP address lookup algorithms can be evaluated on a number of metrics--lookup time, update time, memory usage, and to a less important extent, the time to construct the data structure used to support lookups and updates. Many of the existing methods are(More)
Current biological sequence comparison tools utilize full database searches to find approximate matches between a database and a query. A new approach to sequence comparisons can be performed by indexing the database using a novel indexing scheme. An indexed scheme can immediately eliminate highly mismatched sequences thereby improving performance and(More)
We present faster sequential and parallel algorithms for computing the solvent accessible surface area (ASA) of protein molecules. The ASA is computed by finding the exposed surface areas of the spheres obtained by increasing the van der Waals' radii of the atoms with the van der Waals' radius of the solvent. Using domain specific knowledge, we show that(More)
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