Biological Sequencing and Alignment

Sr. Associate Dr. Bernardo Barbielini Amidei, Department of Physics

THEORY 1: A Model of Evolution (2 hours)

• Markov processes (probability vectors and stochastic matrices).
• Mutation Matrices for amino-acids.
• Dayhoff scoring matrices.

THEORY 2: Sequence alignment (2 hours)

• Dynamic programming.
• Parwise aligment with Dayhoff matrices and gap penalties.

THEORY 3: Phylogenetics trees (2 hours)

• PAM distance.
• tree based on distance matrices.

THEORY 4: Protein Structures by Computation (2 hours)

• Levinthal's paradox.
• Protein threading problem.

LABORATORY 1: Introduction to Unix and Matlab (2 hours)

LABORATORY 2: A Model of Evolution (2 hours)

LABORATORY 3: Sequence alignment (2 hours)

LABORATORY 4: Phylogenetics trees (2 hours)

LABORATORY 5: Protein Structures by Computation (2 hours)