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 O(mn) time and O(m +(More)
We present a parallel algorithm for lexicographically 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)
The Fast Multipole Method (FMM) is a robust technique for the rapid evaluation of the combined e ect of pairwise interactions of n data sources. Parallel computation of the FMM is considered a challenging problem due to the dependence of the computation on the distribution of the data sources, usually resulting in dynamic data decomposition and load(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)
Given two genomic DNA sequences, the syntenic alignment problem is to compute an ordered list of subsequences for each sequence such that the corresponding subsequence pairs exhibit a high degree of similarity. Syntenic alignments are useful in comparing genomic DNA from related species and in identifying conserved genes. In this paper, we present a(More)
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