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1. Introduction
2. Outline
3. Patterns
4. Why pattern discovery?
5. "Ton of data"
6. Sequence patterns: examples
7. Sequence patterns in DNA
8. Pattern representations
9. Pattern representations - consensus sequences
10. Pattern representations - weight matrices
11. Pattern representation: weight matrix
12. Formulae
13. Pattern discovery methods
14. Profile method
15. Profile HMMs
16. Profile HMMs with InDels (1)
17. Profile HMMs with InDels (2)
18. Combinatorial methods
19. Combinatorial method: GYM
20. Example: helix-turn-helix motifs
21. DNA binding at HTH motif
22. Example: HTH motifs and patterns
23. Unaligned pattern discovery
24. TEIRESIAS: key features
25. SPLASH
26. Precomputed sequence patterns
27. Gibbs sampling
28. Expectation maximization (EM)
29. Patterns of protein-DNA interactions
30. Ab initio prediction of TF targets
31. Structure patterns in proteins
32. Structure pattern discovery
33. Sequence-structure patterns
34. Trilogy
35. SSP: supervised pattern discovery algorithm
36. Sequence structure patterns (SSP)
37. Zinc finger motifs: TPs and FPs
38. Limitations in selecting training sets
39. Choosing training sets
40. Conclusions
41. Thanks

Topics Covered

• Why pattern discovery?
• Sequence patterns: representations and protein sequence
• Patterns of DNA-protein interactions
• Structure patterns: representations, discovery and applications
• Sequence-structure patterns
• Designing training sets for supervised discovery
• Algorithmic techniques

Links

Series:

• Using Bioinformatics in the Exploration of Genetic Diversity

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Publication History

• Published on October 1, 2007
• Reviewed on February 8, 2018

Financial Disclosures

• Prof. Giri Narasimhan has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.