Hardness of flip-cut problems from optical mapping

Vlado Dancik, Sridhar Hannenhalli, S. Muthukrishnan

    Research output: Contribution to conferencePaper

    Abstract

    Optical Mapping is a new technology for constructing restriction maps. Associated computational problems include aligning multiple partial restriction maps into a single `consensus' restriction map, and determining the correct orientation of each molecule, which was formalized as the Exclusive Binary Flip Cut (EBFC) Problem by Muthukrishnan and Parida. Here we prove that the EBFC problem, as well as a number of its variants, are NP-Complete. We also identify another problem formalized as Binary Shift Cut (BSC) problem motivated by the fact that there might be missing fragments at the beginnings and/or the ends of the molecules, and prove it to be NP-complete. Therefore, they do not have efficient, that is, polynomial time solutions unless P = NP.

    Original languageEnglish (US)
    Pages275-284
    Number of pages10
    StatePublished - 1997
    EventProceedings of the 1997 International Conference on Compression and Complexity of Sequences - Positano, Italy
    Duration: Jun 11 1997Jun 13 1997

    Conference

    ConferenceProceedings of the 1997 International Conference on Compression and Complexity of Sequences
    CityPositano, Italy
    Period6/11/976/13/97

    ASJC Scopus subject areas

    • Engineering(all)

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  • Cite this

    Dancik, V., Hannenhalli, S., & Muthukrishnan, S. (1997). Hardness of flip-cut problems from optical mapping. 275-284. Paper presented at Proceedings of the 1997 International Conference on Compression and Complexity of Sequences, Positano, Italy, .