Aligning two fragmented sequences

V. Veeramachaneni, P. Berman, W. Miller

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    Upon completion of the human and mouse genome sequences, world-wide sequencing capacity will turn to other complex organisms. Current strategies call for many of these genomes to be incompletely sequenced. That is, holes will remain in the known sequence, and the relative order and orientation of the known sequence fragments may not be determined. Sequence comparison between two genomes of this sort may allow some of the fragments to be oriented and ordered relative to each other by computational means. We formalize this as an optimization problem, show that the problem is MAX-SNP hard, and develop a polynomial time algorithm that is guaranteed to produce a solution whose score is within a factor 3 of optimal.

    Original languageEnglish (US)
    Title of host publicationProceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002
    PublisherInstitute of Electrical and Electronics Engineers Inc.
    Pages187-194
    Number of pages8
    ISBN (Electronic)0769515738, 9780769515731
    DOIs
    StatePublished - Jan 1 2002
    Event16th International Parallel and Distributed Processing Symposium, IPDPS 2002 - Ft. Lauderdale, United States
    Duration: Apr 15 2002Apr 19 2002

    Publication series

    NameProceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002

    Other

    Other16th International Parallel and Distributed Processing Symposium, IPDPS 2002
    CountryUnited States
    CityFt. Lauderdale
    Period4/15/024/19/02

    All Science Journal Classification (ASJC) codes

    • Computer Networks and Communications
    • Modeling and Simulation

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  • Cite this

    Veeramachaneni, V., Berman, P., & Miller, W. (2002). Aligning two fragmented sequences. In Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002 (pp. 187-194). [1016591] (Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/IPDPS.2002.1016591