Finding motifs using random projections

Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Volumn , Issue , 2001, Pages 69-76

  Buhler, J ^a   Tompa, M ^a  

^a University of Washington   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; GENES; SAMPLING;

NUCLEOTIDE SEQUENCES;

MOLECULAR BIOLOGY;

EID: 0034823882     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/369133.369172     Document Type: Conference Paper

References (31)

1. Metal-dependent binding of a factor in vivo to the metal-responsive elements of the metallothionein 1 gene promoter
2. Unsupervised learning of multiple motifs in biopolymers using expectation maximization
3. Algorithms for phylogenetic footprinting
4. An exact algorithm to identify motifs in orthologous sequences from multiple species
5. Positive and negative regulation of the human insulin gene by multiple trans-acting factors
6. Predicting gene regulatory elements in silico on a genomic scale
7. Efficient large-scale sequence comparison by locality-sensitive hashing
8. Maximum likelihood from incomplete data via the EM algorithm
9. Identification of common motifs in unaligned DNA sequences: Application to Escherichia coli Lrp regulon
10. Rigorous pattern-recognition methods for DNA sequences: Analysis of promoter sequences from Escherichia coli
11. Similarity search in high dimensions via hashing
12. Deriving ribosomal binding site (RBS) statistical models from unannotated DNA sequences and the use of the RBS model for N-terminal prediction
13. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
14. Approximate nearest neighbors: Towards removing the curse of dimensionality
15. Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles
16. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
17. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
18. Global self-organization of all known protein sequences reveals inherent biological signatures
19. 1-specific transcription
20. Transcription initiation from the dihydrofolate reductase promoter is positioned by hip1 binding at the initiation site
21. Yy1 facilitates the association of serum response factor with the c-fos serum response element
22. Combinatorial approaches to finding subtle signals in DNA sequences
23. Motif discovery without alignment or enumeration
24. An algorithm for finding novel gapped motifs in DNA sequences
25. Spelling approximate repeated or common motifs using a suffix tree
26. A statistical method for finding transcription factor binding sites
27. Methods for discovering novel motifs in nucleic acid sequences
28. An exact method for finding short motifs in sequences, with application to the ribosome binding site problem
29. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
30. Transfac: A database on transcription factors and their DNA binding sites