On the closest string and substring problems
Journal of the ACM (JACM)
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
On the complexity of finding common approximate substrings
Theoretical Computer Science
Efficient Algorithms for the Closest String and Distinguishing String Selection Problems
FAW '09 Proceedings of the 3d International Workshop on Frontiers in Algorithmics
A simple algorithm for (l, d) motif search
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
More efficient algorithms for closest string and substring problems
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
More Efficient Algorithms for Closest String and Substring Problems
SIAM Journal on Computing
A three-string approach to the closest string problem
Journal of Computer and System Sciences
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We consider the (l,d) Planted Motif Search Problem, a problem that arises from the need to find transcription factor-binding sites in genomic information. We propose the algorithms PMSi and PMSP which are based on ideas considered in PMS1 [10]. These algorithms are exact, make use of less space than the known exact algorithms such as PMS and are able to tackle instances with large values of d. In particular algorithm PMSP is able to solve the challenge instance (17,6), which has not reported solved before in the literature.