Chromosome Reconstruction from Physical Maps Using a Cluster of Workstations

  • Authors:

  • Suchendra Bhandarkar;Salem Machaka

  • Affiliations:

  • Department of Computer Science, University of Georgia, 415 Boyd Graduate Studies Research Center, Athens, GA 30602-7404, USA, suchi@cs.uga.edu;Department of Computer Science, University of Georgia, 415 Boyd Graduate Studies Research Center, Athens, GA 30602-7404, USA, machaka@cs.uga.edu

  • Venue:
  • The Journal of Supercomputing
  • Year:
  • 1997

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Abstract

Ordering clones from a genomic library into physical maps of wholechromosomes presents a central computational problem in genetics. Chromosomereconstruction via clone ordering is shown to be isomorphic to the classicalNP-complete Optimal Linear Arrangement problem. Parallel algorithms forsimulated annealing and microcanonical annealig based on Markov chaindecomposition are proposed and applied to the problem of chromosomereconstruction via clone ordering. These algorithms are implemented on acluster of UNIX workstations using the Parallel Virtual Machine (PVM)system. PVM is a software system that permits a heterogeneous collection ofnetworked computers to be viewed by a user‘s program as a single monolithicparallel computing resource. The parallel algorithms are implemented andtested on clonal data derived from Chromosome IV of the fungus Asperigillusnidulans Perturbation methods and problem-specific annealing heuristics forthe parallel simulated annealing and parallel microcanonical annealingalgorithms are proposed and described. Convergence, speedup and scalabilitycharacteristics of the various parallel algorithms are analyzed anddiscussed.