Aligning two fragmented sequences

Vamsi Veeramachaneni, Piotr Berman, Webb Miller

    Research output: Contribution to journalArticlepeer-review

    5 Scopus citations


    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)
    Pages (from-to)119-143
    Number of pages25
    JournalDiscrete Applied Mathematics
    Issue number1 SPEC.
    StatePublished - Apr 1 2003

    All Science Journal Classification (ASJC) codes

    • Discrete Mathematics and Combinatorics
    • Applied Mathematics


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