Bounds for parametric sequence comparison
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 3(n/2π) 2/3+O(n 1/3 log n) bound on the worst-case number of distinct optimum alignments for two sequences of length n as the parameters are varied....
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| Vydáno v: | Discrete Applied Mathematics Ročník 118; číslo 3; s. 181 - 198 |
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| Hlavní autoři: | , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
Lausanne
Elsevier B.V
15.05.2002
Amsterdam Elsevier New York, NY |
| Témata: | |
| ISSN: | 0166-218X, 1872-6771 |
| On-line přístup: | Získat plný text |
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| Shrnutí: | 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
3(n/2π)
2/3+O(n
1/3
log
n)
bound on the worst-case number of distinct optimum alignments for two sequences of length
n as the parameters are varied. This refines a
O(
n
2/3) upper bound by Gusfield et al., answering a question posed by Pevzner and Waterman. Our lower bound requires an unbounded alphabet. For strings over a binary alphabet, we prove a
Ω(n
1/2)
lower bound. For the parametric global alignment of
k⩾2 sequences under sum-of-pairs scoring we prove a
3((
k
2
)n/2π)
2/3+O(k
2/3n
1/3
log
n)
upper bound on the number of distinct optimality regions and a
Ω(n
2/3)
lower bound, partially answering a problem of Pevzner. Based on experimental evidence, we conjecture that for two random sequences, the number of optimality regions is approximately
n
with high probability. |
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| ISSN: | 0166-218X 1872-6771 |
| DOI: | 10.1016/S0166-218X(01)00206-2 |