Lectures' topics

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September 26^th, 2023

Introduction to Pattern Discovery for Life Sciences.

Big Data: Astronomical or Genomical?

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September 28^th, 2023

Recall of some fundamentals in Biology.

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

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October 03^rd, 2023

Recall of some fundamentals in Biology. Exercises on protein synthesis.

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October 06^th, 2023

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 10^th, 2023

Dynamic Programming algorithms for alignment: Needleman & Wunsch Algorithm.

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October 13^th, 2023

Global alignment through Needleman & Wunsch Algorithm.

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October 20^th, 2023

Needleman & Wunsch Algorithm: coding.

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October 25^th, 2023

Needleman & Wunsch Algorithm: coding.

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October 27^th, 2023

Needleman & Wunsch Algorithm coding in the case of gop and gep.

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November 3^rd, 2023

Smith & Waterman Algorithm.

N&W and S&W Codings.

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November 15^th, 2023

Edit distance and Edit Graphs.

Heuristic algorithms. The filtering technique and Fasta.

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November 17^th, 2023

Fasta and Blast.

Pairwise Alignment biological applications.

Introduction to Multiple Sequence Alignment.

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November 22^nd, 2023

Multiple Sequence Alignment. Algorithms based on Dynamic Programming and their running time. Less expensive alternatives in terms of running time.

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November 24^th, 2023

Greedy and progressive approach. Clustalw. Multiple alignment scoring.

Molecular Evolution. Distance estimation between sequences.

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November 29^th, 2023

Distance estimation between sequences. Molecular clock. Phylogenetic trees. Analysis on the paper "The number of Evolutionary trees" by Joseph Felsenstein.

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December 1^st, 2023

UPGMA. Neighbor Joining.

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December 6^th, 2023

Character state-based optimization trees: maximum parsimony, maximum likelihood. Phylogenetic analysis applications.

Brief analysis on alignment-free methods.

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December 7^th, 2023

Biological Databases and their characteristics. Primary Databases. Pubmed, OMIM.

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December 13^th, 2023

Protein Databases, Specialized Databases. Consensus, patterns, profiles. Introduction to Prosite.

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December 15^th, 2023

Prosite: sintax and some examples. NAR Database Issue.

Introduction to the CG-Island Problem.

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December 20^th, 2023

CG-Islands and Fair-Bet Casino Problem. HMM and Decoding problem. Viterbi Algorithm. Forward-backward problem. Hmm and speech recognition.

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