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Exploring Distant Protein Sequence Relationships

Introduction - Homology and Sequence Similarity
The tree of life - how far back can we see?
Homology and similarity - the globin family
Similarity scores and sequence length
Accurate statistics with Smith-Waterman
Accurate statistics with FASTA
Accurate statistics for DNA
Protein vs DNA sequence comparison
Examining marginal sequence relationships
G-protein coupled receptors
Relationships between G-protein coupled receptors
Linking rhodopsin and secretin/calcitonin families
Beter statistics with higher gap penalties
Relationships between calcium binding proteins
Searching with a short domain
Improvements to FASTA
Summary
Suggested reading

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