A tutorial introduction to
Computational Biochemistry
using Darwin

Gaston H. Gonnet
Informatik E.T.H. Zürich
Switzerland

• Contents
• Interaction with the Darwin system
• Writing functions
• Handling text
• Arrays and lists
• Input/output
• Advanced programming
• Dayhoff matrices and mutation matrices
  • Gap probabilities and gap penalties
  • Computation of matrices
  • Estimating mutation matrices
• Comparing sequences
• All-against-all matching
• Random amino acid sequences
  • Order k stochastic sequences
• Computing estimates of PAM distances
  between species
• Reformatting a database to conform the
  Darwin tagging conventions
• Finding close-to-identical entries
• Building a phylogenetic tree from the results of an all-against-all matching
  • Approximate topology of the tree
  • Evolution phylogenetic trees
  • Generating several ept topologies
• Probabilistic ancestral sequences and multiple alignments
• A model of insertions/deletions
• The GKSKGFGFV sequence
  • Generating random scores
  • Computing expected scores
• Visualization of data
• Families of sequences in a database
• Quick Darwin
• Families of sequences in a database
• Quick Darwin
• About this document ...