Alignments without low-scoring regions

Zheng Zhang, Piotr Berman, Webb Miller

    Research output: Contribution to journalArticlepeer-review

    40 Scopus citations


    Given a strong match between regions of two sequences, how far can the match be meaningfully extended if gaps are allowed in the resulting alignment? The aim is to avoid searching beyond the point that a useful extension of the alignment is likely to be found. Without loss of generality, we can restrict attention to the suffixes of the sequences that follow the strong match, which leads to the following formal problem. Given two sequences and a fixed X > 0, align initial portions of the sequences subject to the constraint that no section of the alignment scores below -X. Our results indicate that computing an optimal alignment under this constraint is very expensive. However, less rigorous conditions on the alignment can be guaranteed by quite efficient algorithms. One of these variants has been implemented in a new release of the Blast suite of database search programs.

    Original languageEnglish (US)
    Pages (from-to)197-210
    Number of pages14
    JournalJournal of Computational Biology
    Issue number2
    StatePublished - 1998

    All Science Journal Classification (ASJC) codes

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


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