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Contents

0. About

1. Algorithms
1.1 Analyzing algorithms
1.2 Input data
1.3 Input size
1.4 Running time
1.5 Memory requirements
1.6 Worst-case and average-case analysis
1.7 Order of growth
1.8 Examples

2. Similarity: basic concepts
2.1 Distances, similarity scores
2.2 String distances
2.3 Approximate string matching; finding optimal alignments
2.4 Motifs as elements of similarity

3. References by subjects
3.1 Algorithms, structure
3.2 Databases: what is on the internet
3.3 Patterns, pattern matching
3.4 Scoring matrices, scoring systems
3.5 Sequence alignment
3.6 Fast database searching
3.7 Multiple sequence alignment
3.8 Protein domain collections