Statistical Physics in Biology

Introduction to Sequence Alignment

1. Sequence comparison
   1. Protein sequences: amino acids and their properties
   2. Why do we need to compare sequences?
      • Find dissimilarities
      • Similar sequences = similar properties
      • Similar sequences = common ancestral genes
   3. Mutations -> Gapless alignments
   4. Mutations, insertions and deletions -> Gapped alignment
2. Sequence alignments
   1. Score = edit distance
   2. Examples of scores
   3. Length of alignment, number of alignments
3. Algorithms for sequence alignments
   1. Dynamics programming
   2. Example
   3. Global and Local alignments
4. BLAST
   1. How it works
   2. Examples