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Course10610857149 lectures

Algorithms in Computational Biology and Sequence Analysis

Prof. Chirag Jain · IISc Bangalore

Start with lecture 1 At NPTEL

Lectures

Week 1 Introduction

  1. Lec 01 Course overview Video
  2. Lec 02 Molecular biology and high-throughput sequencing Video
  3. Lec 03 Data structures/Algorithms Warmup Video
  4. Lec 04 Bitvector rank operations Video
  5. Lec 05 Demo for constructing rank data structure Video

Week 2 Strings and exact matching

  1. Lec 06 Z-algorithm Video
  2. Lec 07 Suffix Arrays Video
  3. Lec 08 Suffix array construction using prefix doubling Video
  4. Lec 09 Demo for constructing suffix array Video

Week 3 Strings and exact matching

  1. Lec 10 Suffix Tree Video
  2. Lec 11 Building Suffix Trees Video
  3. Lec 12 Building Suffix Trees (Continued) Video
  4. Lec 13 Applications of suffix trees Video

Week 4 Strings and exact matching, Pairwise Sequence Alignment

  1. Lec 14 Burrows Wheeler Indexes Video
  2. Lec 15 Burrows Wheeler Indexes (continued) Video
  3. Lec 16 How is BWT useful for indexing genomes? Video
  4. Lec 17 Sequence Alignment and Edit Distance Video
  5. Lec 18 Global and semi-global alignment Video

Week 5 Pairwise Sequence Alignment

  1. Lec 19 Local alignment Video
  2. Lec 20 Scoring gaps in alignments Video
  3. Lec 21 Alignment significance statitstics Video
  4. Lec 22 Alignment demonstration Video

Week 6 Heuristic-based sequence alignment

  1. Lec 23 Heuristics for genome-scale alignment Video
  2. Lec 24 Maximal unique matches Video
  3. Lec 25 Co-linear chaining Video

Week 7 Heuristic-based sequence alignment, Genome reconstruction using graph algorithms

  1. Lec 26 Incorporating gaps into the chaining algorithm Video
  2. Lec 27 IGV Demonstration Video
  3. Lec 28 Genome assembly Video
  4. Lec 29 Shortest common superstring Video

Week 8 Genome reconstruction using graph algorithms

  1. Lec 30 Greedy algorithm for genome assembly Video
  2. Lec 31 Genome assembly using de Bruijn graphs Video
  3. Lec 32 Multiplex de Bruijn graphs and Overlap graphs Video
  4. Lec 33 Assembly Demonstration Video

Week 9 Evolutionary tree reconstruction

  1. Lec 34 Introduction to phylogeny trees Video
  2. Lec 35 Distance based tree reconstruction Video
  3. Lec 36 Character based tree reconstruction Video
  4. Lec 37 Phylogenetic trees Demo Video

Week 10 Probabilistic/machine-learning based sequence models

  1. Lec 38 Hidden Markov Models Video
  2. Lec 39 Hidden Markov Models (contd..) Video
  3. Lec 40 ProtGPT2 Demo Video

Week 11 Pangenome Graphs

  1. Lec 41 Pangenome Graphs Video
  2. Lec 42 Pangenome Demo Video
  3. Lec 43 Multiple Sequence Alignment Video
  4. Lec 44 Multiple Sequence Alignment Demo Video
  5. Lec 45 Sequence alignment to pangenome graphs Video

Week 12 Genomic LLMs and Course Summary

  1. Lec 46 Genomic Large Language Models Video
  2. Lec 47 Course Summary Video

Live Session

  1. Live Session 17-02-2025 Video
  2. Live Session 07-04-2025 Video

Syllabus and materials

At NPTEL, as the course publishes them.

Credits and licence

Institution
IISc Bangalore
Department
Computer Science and Engineering
Teacher
Prof. Chirag Jain
Level
Undergraduate
Language
English
Subjects
Computer science, Engineering
Source
NPTEL
Licence
CC BY-NC-SA, as NPTEL states it. Non-commercial use only. NPTEL's terms
Attribution
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