Lectures' topics
September 25th, 2024
Introduction to Pattern Discovery for Life Sciences.
Big Data: Astronomical or Genomical?
Recall of some fundamentals in Biology: proteins.
September 26th, 2024
Recall of some fundamentals in Biology.
Nucleic acids. Replication, protein synthesis. The Central Dogma of Molecular Biology. Reading Frames. Junk DNA.
Introduction to Alignment. Homology and similarity.
October 03rd, 2024
Exercises on protein synthesis.
Pairwise alignment. Naive algorithm and a very simple way of computing the score.
Pairwise Alignment - gaps allowed: score computation.
October 9th, 2024
Different criteria for evaluating pairings either in the nucleotidic case or in the protein case.
Dynamic Programming algorithms for alignment: Needleman & Wunsch Algorithm.
October 10th, 2024
Global alignment through Needleman & Wunsch Algorithm.
October 16th, 2024
Needleman & Wunsch Algorithm: coding.
October 17th, 2024
Needleman & Wunsch Algorithm: coding.
Smith & Waterman Algorithm.
October 23rd, 2024
Needleman & Wunsch and Smith & Waterman Algorithms : coding.
October 24th, 2024
October 30th, 2024
Edit distance and Edit Graphs.
Heuristic algorithms. The filtering technique and Fasta.
October 31st, 2024
Blast.
Pairwise Alignment biological applications.
Exercises on FastA and Blast.
November 13th, 2024
Multiple Sequence Alignment. Algorithms based on Dynamic Programming and their running time. Less expensive alternatives in terms of running time.
November 14th, 2024
Greedy and progressive approach. Clustalw. Multiple alignment scoring.
Molecular Evolution. Distance estimation between sequences.
November 20th, 2024
Molecular clock hypothesis. Phylogenetic trees. Analysis on the paper "The number of Evolutionary trees" by Joseph Felsenstein.
UPGMA.
November 21st, 2024
Character state-based optimization trees: maximum parsimony, maximum likelihood. Phylogenetic analysis applications.