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CPM
2005
Springer
100views Combinatorics» more  CPM 2005»
10 years 4 months ago
Hardness of Optimal Spaced Seed Design
Abstract. Speeding up approximate pattern matching is a line of research in stringology since the 80’s. Practically fast approaches belong to the class of filtration algorithms,...
François Nicolas, Eric Rivals
CPM
2005
Springer
125views Combinatorics» more  CPM 2005»
10 years 4 months ago
Parametric Analysis for Ungapped Markov Models of Evolution
We present efficient sensitivity-analysis algorithms for two problems involving Markov models of sequence evolution: ancestral reconstruction in evolutionary trees and local ungap...
David Fernández-Baca, Balaji Venkatachalam
CPM
2005
Springer
89views Combinatorics» more  CPM 2005»
10 years 8 months ago
The Median Problem for the Reversal Distance in Circular Bacterial Genomes
Enno Ohlebusch, Mohamed Ibrahim Abouelhoda, Kathri...
CPM
2005
Springer
116views Combinatorics» more  CPM 2005»
10 years 8 months ago
Exact and Approximation Algorithms for DNA Tag Set Design
In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formal...
Ion I. Mandoiu, Dragos Trinca
CPM
2005
Springer
101views Combinatorics» more  CPM 2005»
10 years 8 months ago
Succinct Suffix Arrays Based on Run-Length Encoding
A succinct full-text self-index is a data structure built on a text T = t1t2 . . . tn, which takes little space (ideally close to that of the compressed text), permits efficient se...
Veli Mäkinen, Gonzalo Navarro
CPM
2005
Springer
95views Combinatorics» more  CPM 2005»
10 years 8 months ago
Text Indexing with Errors
Moritz G. Maaß, Johannes Nowak
CPM
2005
Springer
206views Combinatorics» more  CPM 2005»
10 years 8 months ago
A Fast Algorithm for Approximate String Matching on Gene Sequences
Abstract. Approximate string matching is a fundamental and challenging problem in computer science, for which a fast algorithm is highly demanded in many applications including tex...
Zheng Liu, Xin Chen, James Borneman, Tao Jiang
CPM
2005
Springer
105views Combinatorics» more  CPM 2005»
10 years 8 months ago
Reducing the Size of NFAs by Using Equivalences and Preorders
Abstract. The efficiency of regular expression matching algorithms depends very much on the size of the nondeterministic finite automata (NFA) obtained from regular expressions. R...
Lucian Ilie, Roberto Solis-Oba, Sheng Yu
CPM
2005
Springer
109views Combinatorics» more  CPM 2005»
10 years 8 months ago
Using PQ Trees for Comparative Genomics
Permutations on strings representing gene clusters on genomes have been studied earlier in [18, 14, 3, 12, 17] and the idea of a maximal permutation pattern was introduced in [12]....
Gad M. Landau, Laxmi Parida, Oren Weimann
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