Lectures' topics

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September 22^nd, 2026

Introduction to Pattern Discovery for Life Sciences. Big Data: Astronomical or Genomical?

Recall on some fundamentals in Biology: proteins.

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September 28^th, 2026

Recall of some fundamentals in Biology: DNA, RNA.

Replication, protein synthesis. The Central Dogma of Molecular Biology. Reading Frames. Junk DNA.

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September 29^th, 2026

Exercises on protein synthesis.

Introduction to Alignment. Homology and similarity.

Pairwise alignment. Naive algorithm and a very simple way of computing the score.

Pairwise Alignment - gaps allowed: score computation.

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October 05^th, 2026

Different criteria for evaluating pairings either in the nucleotidic case or in the protein case.

Substitution matrices.

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October 06^th, 2026

Dot plots matrices.

Dynamic Programming algorithms for alignment: Needleman & Wunsch Algorithm.

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October 12^th, 2026

Global alignment through Needleman & Wunsch Algorithm. Local alignment through Smith & Waterman algorithm.

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October 13^th, 2026

Needleman & Wunsch Algorithm coding.

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October 19^th, 2026

Needleman & Wunsch Algorithm coding.

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October 20^th, 2026

Needleman & Wunsch Algorithm coding.

Edit distance and Edit Graphs. Introduction to the heuristic algorithms.

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October 26^th, 2026

"A general method applicable to the search for similarities in the amino acid sequence of two proteins", by Needleman and Wunsch.

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October 27^th, 2026

Needleman & Wunsch and Smith Waterman Algorithms coding.

Heuristic algorithms. The filtering technique. FastA.

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November 2^nd, 2026

Blast. Pairwise Alignment biological applications.

Multiple Sequence Alignment. Algorithms based on Dynamic Programming and their running time.

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November 3^rd, 2026

Less expensive alternatives in terms of running time.

Greedy and progressive approach. Clustalw. Multiple alignment scoring.

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