Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
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
Masking patterns in sequences: A new class of motif discovery with don't cares
Theoretical Computer Science
Suffix tree characterization of maximal motifs in biological sequences
Theoretical Computer Science
MADMX: a novel strategy for maximal dense motif extraction
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
| Hi-index | 0.00 |
We investigate the structure of the set of gapped motifs (repeated patterns with don't cares) of a given string of symbols. A natural equivalence classification is introduced for the motifs, based on their pattern of occurrences, and another classification for the occurrence patterns, based on the induced motifs. Quadratic-time algorithms are given for finding a maximal representative for an equivalence class while the problems of finding a minimal representative are shown NP-complete. Maximal gapped motifs are shown to be composed of blocks that are maximal non-gapped motifs. These can be found using suffix-tree techniques. This leads to a bound on the number of gapped motifs that have a fixed number of non-gapped blocks.