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September 25, 2023

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Description

ECS 124: Fundamental Algorithms in Bioinformatics (UC Davis). Instructor: Professor Dan Gusfield.

This course covers fundamental algorithms for efficient analysis of biological sequences and for building evolutionary trees. This is an undergraduate course taught by UC Davis computer science professor Dan Gusfield focusing on the ideas and concepts behind the most central algorithms in biological sequence analysis. Dynamic Programming, Alignment, Hidden Markov Models, Statistical Analysis are emphasized.

The videos were mostly made in 2002 and edited and somewhat extended in 2014. Despite their age, and despite the fact that "software, databases, websites, and data" in bioinformatics change rapidly, the topics included are still of current importance.

Course Curriculum

  • Lecture 01 – Introduction to Bioinformatics and the Course Unlimited
  • Lecture 02 – Further Introduction Unlimited
  • Lecture 03 – Defining Sequence Similarity Unlimited
  • Lecture 04 – Extending the Model of Sequence Similarity Unlimited
  • Lecture 05 – Computing Sequence Similarity Unlimited
  • Lecture 06 – Computing Similarity Using Alignment Graph Unlimited
  • Lecture 07 – From Alignment Graphs to Formal Dynamic Programming Unlimited
  • Lecture 08 – Sequence Alignment Using Dynamic Programming (cont.) Unlimited
  • Lecture 09 – Local Sequence Alignment Unlimited
  • Lecture 10 – End-gap Free Alignment and Whole-genome Shotgun Sequencing Unlimited
  • Lecture 11a – Expected Length of the Longest Common Subsequence Unlimited
  • Lecture 11b – Expected Length of the Longest Common Substring Unlimited
  • Lecture 12 – Expected Longest Common Substring II Unlimited
  • Lecture 13 – Probability of a Complete Query Match in a Database Unlimited
  • Lecture 14 – BLAST (Basic Local Alignment Search Tool) I Unlimited
  • Lecture 15 – BLAST II Unlimited
  • Lecture 16 – BLAST Statistics Unlimited
  • Lecture 17 – Probability and Database Search Unlimited
  • Lecture 18 – Multiple Sequence Alignment I Unlimited
  • Lecture 19 – Multiple Sequence Alignment II Unlimited
  • Lecture 20 – Multiple Sequence Alignment III Unlimited
  • Lecture 21 – Uses of Multiple Sequence Alignment Unlimited
  • Lecture 22 – From Profiles to Markov Models Unlimited
  • Lecture 23 – Hidden Markov Models Unlimited
  • Lecture 24 – Hidden Markov Models and the Viterbi Algorithm Unlimited
  • Lecture 25 – From the Viterbi Algorithm to the Forward Algorithm Unlimited
  • Lecture 26 – Hidden Markov Models – The Backwards Algorithm Unlimited
  • Lecture 27 – Introduction to Evolutionary Trees – Ultrametric Trees Unlimited
  • Lecture 28 – Algorithms for Ultrametric Trees – Molecular Clocks Unlimited
  • Lecture 29 – Additive Trees and the Neighbor-Joining Algorithm Unlimited
  • Lecture 30 – Maximum Parsimony and Minimum Mutation Methods Unlimited

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