The parameterized complexity of sequence alignment and consensus
Theoretical Computer Science
On the Approximation of Shortest Common Supersequencesand Longest Common Subsequences
SIAM Journal on Computing
Finding similar regions in many strings
STOC '99 Proceedings of the thirty-first annual ACM symposium on Theory of computing
Distinguishing string selection problems
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
The Complexity of Some Problems on Subsequences and Supersequences
Journal of the ACM (JACM)
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
On the Parameterized Intractability of CLOSEST SUBSTRINGsize and Related Problems
STACS '02 Proceedings of the 19th Annual Symposium on Theoretical Aspects of Computer Science
Systematic parameterized complexity analysis in computational phonology
Systematic parameterized complexity analysis in computational phonology
Parameterized Complexity
Hard problems in similarity searching
Discrete Applied Mathematics - Discrete mathematics & data mining (DM & DM)
The Closest Substring problem with small distances
FOCS '05 Proceedings of the 46th Annual IEEE Symposium on Foundations of Computer Science
An Exact Data Mining Method for Finding Center Strings and All Their Instances
IEEE Transactions on Knowledge and Data Engineering
Fast and Practical Algorithms for Planted (l, d) Motif Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Faster Algorithms for Sampling and Counting Biological Sequences
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Hard problems in similarity searching
Discrete Applied Mathematics
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
An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Slightly superexponential parameterized problems
Proceedings of the twenty-second annual ACM-SIAM symposium on Discrete Algorithms
Space and time efficient algorithms for planted motif search
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
An improved voting algorithm for planted (l,d) motif search
Information Sciences: an International Journal
| Hi-index | 5.23 |
Problems associated with finding strings that are within a specified Hamming distance of a given set of strings occur in several disciplines. In this paper, we use techniques from parameterized complexity to assess non-polynomial time algorithmic options and complexity for the COMMON APPROXIMATE SUBSTRING (CAS) problem. Our analyses indicate under which parameter restrictions useful algorithms are possible, and include both class membership and parameterized reductions to prove class hardness. In order to achieve fixed-parameter tractability, either a fixed string length or both a fixed size alphabet and fixed substring length are sufficient. Fixing either the string length or the alphabet size and Hamming distance is shown to be necessary, unless W[1] = FPT. An assortment of parameterized class membership and hardness results cover all other parameterized variants, showing in particular the effect of fixing the number of strings.