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Author Eppstein, David ♦ Galil, Zvi ♦ Giancarlo, Raffaele ♦ Italiano, Giuseppe F.
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©1992
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Dynamic programming ♦ Recurrence ♦ Sequence alignment ♦ Sparsity ♦ Time complexity
Abstract Dynamic programming solutions to two recurrence equations, used to compute a sequence alignment from a set of matching fragments between two strings, and to predict RNA secondary structure, are considered. These recurrences are defined over a number of points that is quadratic in the input size; however, only a sparse set matters for the result. Efficient algorithms are given for solving these problems, when the cost of a gap in the alignment or a loop in the secondary structure is taken as a convex or concave function of the gap or loop length. The time complexity of our algorithms depends almost linearly on the number of points that need to be considered; when the problems are sparse, this results in a substantial speed-up over known algorithms.
ISSN 00045411
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 1992-07-01
Publisher Place New York
e-ISSN 1557735X
Journal Journal of the ACM (JACM)
Volume Number 39
Issue Number 3
Page Count 22
Starting Page 546
Ending Page 567


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Source: ACM Digital Library