Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing
Reducing the space requirement of suffix trees
Software—Practice & Experience
Journal of Algorithms
Succinct representations of lcp information and improvements in the compressed suffix arrays
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Succinct Representation of Balanced Parentheses and Static Trees
SIAM Journal on Computing
Compressed Text Databases with Efficient Query Algorithms Based on the Compressed Suffix Array
ISAAC '00 Proceedings of the 11th International Conference on Algorithms and Computation
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Opportunistic data structures with applications
FOCS '00 Proceedings of the 41st Annual Symposium on Foundations of Computer Science
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
Engineering a compressed suffix tree implementation
Journal of Experimental Algorithmics (JEA)
Engineering a compressed suffix tree implementation
WEA'07 Proceedings of the 6th international conference on Experimental algorithms
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
Rapid homology search with two-stage extension and daughter seeds
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
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We show space-economical algorithms for finding maximal unique matches (MUM's) between two strings which are important in large scale genome sequence alignment problems. Our algorithms require only O(n) bits (O(n/ log n) words) where n is the total length of the strings. We propose three algorithms for different inputs: When the input is only the strings, their compressed suffix array, or their compressed suffix tree. Their time complexities are O(n log n), O(n log驴n) and O(n) respectively, where 驴 is any constant between 0 and 1. We also show an algorithm to construct the compressed suffix tree from the compressed suffix array using O(n log驴n) time and O(n) bits space.