Four Strikes Against Physical Mapping of DNA

Paul W. Goldberg, Martin C. Golumbic, Haim Kaplan, Ron Shamir

Research output: Contribution to journalArticlepeer-review

Abstract

Physical mapping is a central problem in molecular biology and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NP-complete decision problems: Colored unit interval graph completion, the maximum interval (or unit interval) subgraph, the pathwidth of a bipartite graph, and the k -consecutive ones problem for k ≥ 2. These models have been chosen to reflect various features typical in biological data, including false-negative and positive errors, small width of the map, and chimericism.

Original languageEnglish
Pages (from-to)139-152
Number of pages14
JournalJournal of Computational Biology
Volume2
Issue number1
DOIs
StatePublished - 1995

Keywords

  • NP-completeness
  • interval graphs
  • k-consecutive ones problem
  • physical mapping

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