Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization
Machine Learning - Special issue on applications in molecular biology
Finding motifs using random projections
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Finding motifs in the twilight zone
Proceedings of the sixth annual international conference on Computational biology
Proceedings of the sixth annual international conference on Computational biology
Finding similar regions in many sequences
Journal of Computer and System Sciences - STOC 1999
Modeling dependencies in protein-DNA binding sites
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
A Statistical Method for Finding Transcription Factor Binding Sites
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
cWINNOWER Algorithm for Finding Fuzzy DNA Motifs
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Finding short DNA motifs using permuted markov models
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Finding motifs for insufficient number of sequences with strong binding to transcription facto
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Enhanced position weight matrices using mixture models
Bioinformatics
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
Generalized planted (l,d)-motif problem with negative set
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Overlap-Based Similarity Metrics for Motif Search in DNA Sequences
ICONIP '09 Proceedings of the 16th International Conference on Neural Information Processing: Part II
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The problem of discovering novel motifs of binding sites is important to theunderstanding of gene regulatory networks. Motifs are generally represented by matrices (PWM orPSSM) or strings. However, these representations cannot model biological binding sites wellbecause they fail to capture nucleotide interdependence. It has been pointed out by manyresearchers that the nucleotides of the DNA binding site cannot be treated independently, e.g. thebinding sites of zinc finger in proteins. In this paper, a new representation called Scored PositionSpecific Pattern (SPSP), which is a generalization of the matrix and string representations, isintroduced which takes into consideration the dependent occurrences of neighboring nucleotides.Even though the problem of discovering the optimal motif in SPSP representation is proved to beNP-hard, we introduce a heuristic algorithm called SPSP-Finder, which can effectively findoptimal motifs in most simulated cases and some real cases for which existing popular motiffindingsoftware, such as Weeder, MEME and AlignACE, fail.