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IJCAI
2003
13 years 10 months ago
Comparing Best-First Search and Dynamic Programming for Optimal Multiple Sequence Alignment
Sequence alignment is an important problem in computational biology. We compare two different approaches to the problem of optimally aligning two or more character strings: bounde...
Heath Hohwald, Ignacio Thayer, Richard E. Korf
ICALP
1995
Springer
14 years 11 days ago
Weakly Useful Sequences
An infinite binary sequence x is defined to be (i) strongly useful if there is a computable time bound within which every decidable sequence is Turing reducible to x; and (ii) w...
Stephen A. Fenner, Jack H. Lutz, Elvira Mayordomo
SPIRE
2005
Springer
14 years 2 months ago
Normalized Similarity of RNA Sequences
We introduce a normalized version of the LCS metric as a new local similarity measure for comparing two RNAs. An O(n2 m lg m) time algorithm is presented for computing the maximum ...
Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren...
ICCD
2003
IEEE
109views Hardware» more  ICCD 2003»
14 years 5 months ago
Independent Test Sequence Compaction through Integer Programming
We discuss the compaction of independent test sequences for sequential circuits. Our first contribution is the formulation of this problem as an integer program, which we then so...
Petros Drineas, Yiorgos Makris
SODA
2000
ACM
106views Algorithms» more  SODA 2000»
13 years 10 months ago
Algorithms for optimizing production DNA sequencing
We discuss the problem of optimally "finishing" a partially sequenced, reconstructed DNA segment. At first sight, this appears to be computationally hard. We construct a...
Éva Czabarka, Goran Konjevod, Madhav V. Mar...