On finding lowest common ancestors: simplification and parallelization
SIAM Journal on Computing
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
An algorithm for finding novel gapped motifs in DNA sequences
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Spelling Approximate Repeated or Common Motifs Using a Suffix Tree
LATIN '98 Proceedings of the Third Latin American Symposium on Theoretical Informatics
Color Set Size Problem with Application to String Matching
CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
Approximate String-Matching over Suffix Trees
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Numerical Recipes 3rd Edition: The Art of Scientific Computing
Numerical Recipes 3rd Edition: The Art of Scientific Computing
Finding Higher Order Motifs under the Levenshtein Measure
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
On the longest common rigid subsequence problem
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
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Using our techniques for extracting approximate nontandem repeats[1] on well constructed maximal models, we derive an algorithm to find common motifs of length P that occur in N sequences with at most D differences under the Edit distance metric. We compare the effectiveness of our algorithm with the more involved algorithm of Sagot[17] for Edit distance on some real sequences. Her method has not been implemented before for Edit distance but only for Hamming distance[12,20]. Our resulting method turns out to be simpler and more efficient theoretically and also in practice for moderately large P and D.