Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
Mining Motifs in Massive Time Series Databases
ICDM '02 Proceedings of the 2002 IEEE International Conference on Data Mining
Algorithmic techniques in computational genomics
Algorithmic techniques in computational genomics
Bases of Motifs for Generating Repeated Patterns with Wild Cards
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Theoretical Computer Science
Incremental discovery of the irredundant motif bases for all suffixes of a string in O(n2logn) time
Theoretical Computer Science
Pattern Discovery in Bioinformatics: Theory & Algorithms
Pattern Discovery in Bioinformatics: Theory & Algorithms
Extracting approximate patterns
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
MADMX: a novel strategy for maximal dense motif extraction
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Characterization and extraction of irredundant tandem motifs
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
Discrete Applied Mathematics
| Hi-index | 5.23 |
Bases of generators of motifs consisting of strings in which some positions can be occupied by a don't care provide a useful conceptual tool for their description and a way to reduce the time and space involved in the discovery process. In the last few years, a few algorithms have been proposed for the extraction of a basis, building in large part on combinatorial properties of strings and their autocorrelations. Currently, the most efficient techniques for binary alphabets and quorum q=2 require time quadratic in the length of the host string. The present paper explores properties of motif bases for quorum q=2, both with binary and general alphabets, by also showing that important results holding for quorum q=2 cannot be extended to this, more general, case. Furthermore, the extraction of motifs in which a bound is set on the maximum allowed number of don't cares is addressed, and suitable algorithms are proposed whose computational complexity depends on the fixed bound.