Table of Contents
Methods for the automatic discovery of patterns in sequences
Overview of talk
Families, patterns, motifs
Prosite: Patterns for classification
Example sequence motif (zinc finger c2h2)
Motif Usage
Protein Sequence Motif Databases
InterPro - EU funded collaboration between the databases
Motifs in Protein Analysis
Strategy for developing motifs
PPT Slide
A three steps Approach to Pattern Discovery
Pattern Languages
Different description languages
The advantages and disadvantages of deterministic patterns
Evaluating patterns
Examples of Fitness Functions
Algorithms for pattern discovery
Approaches to pattern discovery
Pattern Driven - pruning the search space
An Example Algorithm: Pratt
Pratt - solution space
An Example Algorithm: Pratt
Pratt - Pattern scoring
An Example Algorithm: Pratt
Pratt - Search
Pratt - functionality
Pratt - Example
Pratt in the InterPro project
Structure Motif Discovery
SPratt - Search based algorithm for discovering Structure Motifs
SPratt - Idea
Structure - represent each residue’s neighbourhood
Mark all residues within d Angstrom
Make neighbour string - C-terminal direction
Make neighbour string - N-terminal direction
SPratt - Neighbour Strings
SPratt - discovery algorithm
Example output: Cystein proteases
RMSd matrix
SPratt: Structures ? Motif
Combining SPratt with SAP
SAP output - cystein proteases
SAP output - 2Fe2S Ferrodoxins
Test Cases - Summary of SPratt runs
Expression Profiler
Cluster Genes
EPCLUST
Retrieve Upstreams
Retrieve Upstream Regions
Mine for Regulatory Signals
SPEXS - Sequence Pattern EXhaustive Search
Large Scale Experiment on Yeast
Gene Clusters
Pattern Score vs. Cluster Score
Randomized data
PPT Slide
Large Scale Experiment - Conclusions
Expression Profiler Web-tool
PPT Slide
Acknowledgements
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