1- Protein coding genes in genomic sequences
   -fasta file, multifasta file
   -uniprot
   -BLAT


2- Homology
   -homology intro: homology, similarity, analogy (examples) 
    Ontogenetic homology: early embryonic development
   -secuence, structure, function
   -the Rost curve
   -paralogy (gene duplication), orthology (speciation)
   -convergent evolution
   -horizontal gene transfer
   -first protein sequence against a database search (Russell F. Doolittle)
   -protein. relation between: sequence, structure and function
   -BLAST


3-Multiple sequence alignment (MAS)

   -Introduction to alignment
   -Introduction to sequence alignment
   -why is good to perform a MAS?
   -pairwise alignment
   -basic metrics: Hamming, Levenshtein
   -scoring schemes, scoring matrices (Dayhoff PAM, BLOSUM)
   -concept of gaps in an alignment
   -global alignment (Needleman and Wunsch)
    local alignment (Smith and Waterman)
   -multiple sequence alignment versus pairwise alignment
   -pairwise alignment, different methods and applications
   -dynamic programming, from the manhattan graph problem to seq. alignment
    dynamic programming computational complexity and the necessity of using heuristics
    What is an heuristic?
   -word methods for pairwise alignment: BLAST, FASTA
   -sequence alignment profiles. sequence logos
   -can we align a profile against a sequence?. can we align a profile against a profile?
   -multiple sequence alignment, the greedy algorithm


4.-Phylogeny
   
   -taxonomy, evolution and phylogeny definition
   -homology, similarity, clustering and hierarchical clustering
   -phylogenetic trees (unrooted and rooted, examples)
   -earlier phylogenetic studies from the molecular evolution perspective
      -phylogenetic study on fishes (Reichert and Brown 1909)      
      -divergence between chimp and humans
      -the 3rd kingdom of life: Arkaea (Woese)
      -modern mitochondrial DNA in forensic studies
   -what is a tree? (from graphs)
   -building phylogenetic trees: phenetic and cladistic approach
   -UPGMA method
   -maximum parsimony method
   -varying rates of evolution (lizards, cocrodiles and birds)
   -time Tree: the timescale of life  


5.-Protein structure

   -central dogma of Molecular Biology
   -amino acids, polypeptides
   -chemical properties of the amino acids, classification
   -protein structure (different chemical interactions)
   -protein structure: primary, secondary, tertiary, quaternary structures.
   -protein folding problem
      Levinthal's paradox
      Anfinsen's dogma
   -relation between: prot. sequence, prot. structure and prot. function

6.- PDB (protein data bank)
    -intro to the data Bank.
    -evolution of the database
    -current state, diff. experimental method contributions
    -X-ray crystallography
    -nuclear magnetic resonance
    -electron microscopy
    -RCSB PDB, what can I retrieve from a PDB id?
    -pdf text file description
    -graphical tools for visualization: Chimera