Approximate nearest neighbors: towards removing the curse of dimensionality
STOC '98 Proceedings of the thirtieth annual ACM symposium on Theory of computing
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
An Efficient Algorithm for the Extended (l, d)-Motif Problem with Unknown Number of Binding Sites
BIBE '05 Proceedings of the Fifth IEEE Symposium on Bioinformatics and Bioengineering
Bioinformatics
Fast and Practical Algorithms for Planted (l, d) Motif Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Bioinformatics
A Monte Carlo EM Algorithm for De Novo Motif Discovery in Biomolecular Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Generalized planted (l,d)-motif problem with negative set
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
| Hi-index | 0.98 |
Planted (l,d)-motif identification is an important and challenging problem in computational biology. In this paper, we present an original algorithm (GARPS) that combines Genetic Algorithm (GA) and Random Projection Strategy (RPS) to identify (l,d)-motifs. We start with RPS to find good starting positions by introducing position-weighted function and hash each of all l-mers in the input sequences onto the corresponding k-dimensional (k