Sridhar Chirravuri

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In this paper we present our practical experience with the design and implementation of a suite of parallel algorithms called PARODS, for chromosome reconstruction via ordering of DNA sequences. PARODS contains parallel algorithms based on an earlier serial algorithm ODS which is a physical mapping algorithm based on simulated annealing. The parallel(More)
Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational problem in genetics. Chromosome reconstruction via clone ordering is shown to be isomorphic to the NP-complete Optimal Linear Ordering problem. Massively parallel algorithms for simulated annealing based on Markov chain distribution are proposed(More)
Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational problem in genetics. Chromosome reconstruction via clone ordering is usually isomorphic to the NP-complete Optimal Linear Arrangement problem. Parallel SIMD and MIMD algorithms for simulated annealing based on Markov chain distribution are(More)
The Kz entropy, and the correlation dimension are commonly used measures of chaotic activity in com.-plea: dynamic systems. The design and implem,enta-tion of a massively parallel algorithm on the Mas-Par MP-2 for the computation of Kz entropy and the correlation dimension is presented. The algorithm is used to compute the Kz entropy and correlation(More)
A suite of parallel algorithms for ordering DNA sequences (termed PARODS) is presented. The algorithms in PARODS are based on an earlier serial algorithm, ODS, which is a physical mapping algorithm based on simulated annealing. Parallel algorithms for simulated annealing based on Markov chain decomposition are proposed and applied to the problem of physical(More)
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