Winnowing sequences from a database search

Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller

    Research output: Contribution to journalReview articlepeer-review

    4 Scopus citations


    In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of 'tolerable redundancy.' An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.

    Original languageEnglish (US)
    Pages (from-to)293-302
    Number of pages10
    JournalJournal of Computational Biology
    Issue number1-2
    StatePublished - 2000

    All Science Journal Classification (ASJC) codes

    • Modeling and Simulation
    • Molecular Biology
    • Genetics
    • Computational Mathematics
    • Computational Theory and Mathematics


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