1- Protein coding genes in genomic sequences -fasta file, multifasta file -Uniprot -DNA Fountain: a new method for storing information on DNA -BLAT 2- 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 3-Multiple sequence alignment (MAS) -Introduction to alignment -Classical alignment representation: * (identity), : (conserved), . (semi-conserved), blank (mismatch) -bisulphite sequencying -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 tree (data structure) -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, 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 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? -PDB text file description -graphical tools for visualization: Chimera