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MODELS OF PROTEIN EVOLUTION: AN INTRODUCTION TO AMINO ACID EXCHANGE MATRICES

MODELS OF PROTEIN EVOLUTION: AN INTRODUCTION TO AMINO ACID EXCHANGE MATRICES. Robert Hirt Institute for Cell and Molecular Biosciences, Newcastle University, UK. Inferring trees is difficult!!!. 1. The method problem. A. Method 1. Dataset 1. B. ?. C. A. Method 2. C. Dataset 1. B.

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Scoring Matrices

Scoring Matrices. Diff. Scoring Rules Lead to Diff. Alignments. Example Score = 5 x (# matches) + (-4) x (# mismatches) + + (-7) x (total length of all gaps) Example Score = 5 x (# matches) + (-4) x (# mismatches) + + (-5) x (# gap openings) + (-2) x (total length of all gaps).

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Acid substitution matrices - PowerPoint PPT Presentation

MODELS OF PROTEIN EVOLUTION: AN INTRODUCTION TO AMINO ACID EXCHANGE MATRICES

Scoring Matrices