Table of Contents
Applying the Pratt pattern discovery program to analysis of protein and DNA sequences
Families, patterns, motifs
Prosite: Patterns for classification
Example sequence motif (zinc finger c2h2)
Strategy for developing motifs
PPT Slide
Pattern from alignment
A three steps Approach to Pattern Discovery
An Example Algorithm: Pratt
Pratt - solution space
An Example Algorithm: Pratt
An Example Algorithm: Pratt
Pratt - Search
Pratt Two-phase Pattern Search - Example
Pratt - functionality
Pratt - Example
Using Pratt
Choice of interfaces
Demo
Pattern Discovery in DNA sequences
Expression Profiler
Example: Diauxic Shift (DeRisi et al 1997)
Organization of a typical yeast promoter
Cluster of co- expressed genes
Discover Patterns in Upstream Regions
Mine for Regulatory Signals
SPEXS - Sequence Pattern EXhaustive Search
Demo
Pattern Score vs. Cluster Score
Randomized data
PPT Slide
Conclusion
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Author: Inge Jonassen
Email: inge@ii.uib.no
Home Page: http://www.ii.uib.no/~inge
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