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
Monotony of surprise and large-scale quest for unusual words
Proceedings of the sixth annual international conference on Computational biology
An Output-Sensitive Flexible Pattern Discovery Algorithm
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Bases of Motifs for Generating Repeated Patterns with Wild Cards
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Longest repeats with a block of k don't cares
Theoretical Computer Science
A polynomial space and polynomial delay algorithm for enumeration of maximal motifs in a sequence
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
Efficient construction of maximal and minimal representations of motifs of a string
Theoretical Computer Science
Characterization and extraction of irredundant tandem motifs
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
Hi-index | 5.23 |
The problems of finding maximal and minimal equivalent representations for gapped and non-gapped motifs as well as finding motifs that characterize a fixed set of occurrence locations for a given string are studied. We apply two equivalence relations on representations. The first one is the well-known occurrence-equivalence of motifs. The second equivalence is introduced for patterns of occurrence locations, to characterize such patterns by motifs. For both equivalences, quadratic-time algorithms are given for finding a maximal representative of an equivalence class. Finding a minimal representative is shown to be NP-complete in both cases. For non-gapped motifs suffix-tree-based linear-time algorithms are given for finding maximal and minimal representatives. Maximal (minimal) gapped motifs are composed of blocks that are maximal (minimal) non-gapped motifs, maximal and minimal non-gapped motifs thus making up a small basis for all motifs. The implied bound on the number of gapped motifs that have a fixed number of non-gapped blocks is also given.