Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Spelling Approximate Repeated or Common Motifs Using a Suffix Tree
LATIN '98 Proceedings of the Third Latin American Symposium on Theoretical Informatics
Fast and Practical Algorithms for Planted (l, d) Motif Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient composite pattern finding from monad patterns
International Journal of Bioinformatics Research and Applications
RISOTTO: fast extraction of motifs with mismatches
LATIN'06 Proceedings of the 7th Latin American conference on Theoretical Informatics
| Hi-index | 0.00 |
In this paper we present an algorithm for the problem of planted structured motif extraction from a set of sequences. This problem is strictly related to the structured motif extraction problem, which has many important applications in molecular biology. We propose an algorithm that uses a simple two-stage approach: first it extracts simple motifs, then the simple motifs are combined in order to extract structured motifs. We compare our algorithm with existing algorithms whose code is available, and which are based on more complex approaches. Our experiments show that, even if in general the problem is NP-hard, our algorithm is able to handle complex instances of the problem in a reasonable amount of time.