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String Processing and Information Retrieval, International Symposium on (1999)
Cancun, Mexico
Sept. 21, 1999 to Sept. 24, 1999
ISBN: 0-7695-0268-7
pp: 55
David Fernandez-Baca , Iowa State University
Timo Seppalainen , Iowa State University
Giora Slutzki , Iowa State University
We consider the problem of computing a global alignment between two or more sequences subject to varying mismatch and indel penalties. We prove a tight \mathbound on the worst-case number of distinct optimum alignments for two sequences of length n as the parameters are varied. This refines a \mathupper bound by Gusfield et al. Our lower bound requires an unbounded alphabet. For strings over a binary alphabet, we prove a \mathlower bound. For the parametric global alignment of \mathsequences under sum-of-pairs scoring we prove a \mathupper bound on the number of distinct optimality regions and a \mathlower bound. Based on experimental evidence, we conjecture that for two random sequences, the number of optimality regions is approximately \mathwith high probability.
Sequence comparison, global alignments, sensitivity analysis, parametric computing, computational biology

G. Slutzki, T. Seppalainen and D. Fernandez-Baca, "Bounds for Parametric Sequence Comparison," String Processing and Information Retrieval, International Symposium on(SPIRE), Cancun, Mexico, 1999, pp. 55.
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