Massively parallel algorithms for chromosome reconstruction.

S M Bhandarkar; S Chirravuri; J Arnold; D Whitmire

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PubMed · 9390225

Massively parallel algorithms for chromosome reconstruction.

S M Bhandarkar·S Chirravuri·J Arnold·D Whitmire

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Abstract

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 and applied to this problem. Perturbation methods and problem-specific annealing heuristics are proposed and described. Experimental results on a 2048 processor MasPar MP-2 system are presented. Convergence, speedup and scalability characteristics of the various algorithms are analyzed and discussed.

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Algorithms Chromosomes Cloning, Molecular Computer Simulation DNA Genetic Techniques Genomic Library Markov Chains Software Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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S M Bhandarkar, S Chirravuri, J Arnold, D Whitmire. 1996. Massively parallel algorithms for chromosome reconstruction.. https://pubmed.ncbi.nlm.nih.gov/9390225/

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