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


2- Multiple sequence alignment (MAS)
   -introduction to alignment
   -Classical alignment representation: * (identity), : (conserved), . (semi-conserved), blank (mismatch)
   -bisulphite sequencing
   -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 algorithm


3- Homology
   -homology intro: homology, similarity, analogy (examples) 
   -secuence, structure, function
   -the Rost curve
   -gene duplication, speciation
   -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, BLASTP


4- Protein structure

   -central dogma of Molecular Biology
   -amino acids, polypeptides
   -chemical properties of the amino acids, classification
   -protein structure (different chemical interactions, dissociations energies)
   -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


5.- 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?
    -PDB text file description
    -graphical tools for visualisation: Chimera