Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
PRUNER: Algorithms for Finding Monad Patterns in DNA Sequences
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
DNA Motif Representation with Nucleotide Dependency
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An efficient motif discovery algorithm with unknown motif length and number of binding sites
International Journal of Data Mining and Bioinformatics
Finding motifs using harmony search
ISB '10 Proceedings of the International Symposium on Biocomputing
Bouma2: a high-performance input-aware multiple string-match algorithm
CIAA'11 Proceedings of the 16th international conference on Implementation and application of automata
Generalized planted (l,d)-motif problem with negative set
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
| Hi-index | 0.00 |
The c WINNOWER algorithm detects.fuzzy motifs in DNAsequences rich in protein-binding signals. A signal is definedas any short nucleotide pattern having up to d mutationsdiffering from a motif of length l. The algorithm findssuch motifs ifmultiple mutated copies of the motif (i.e., thesignals) are present in the DNA sequence in sufficient abundance.The cWINNOWER algorithm substantially improvesthe sensitivity of the winnower method of Pevzner and Szeby imposing a consensus constraint, enabling it to detectmuch weaker signals. We studied the minimum number ofdetectable motifs qc as a function of sequence length N forrandom sequences. We found that qc increases linearly withN for a fast version of the algorithm based on countingthree-member sub-cliques. Imposing consensus constraintsreduces qc by a factor of three in this case, which makes thealgorithm dramatically more sensitive. Our most sensitivealgorithm, which counts four-member sub-cliques, needs aminimum of only 13 signals to detect motifs in a sequenceof length N = 12000 for (l,d) = (15,4).