# Algorithms in Computational Biology and Sequence Analysis

- Institution: IISc Bangalore
- Department: Computer Science and Engineering
- Teacher: Prof. Chirag Jain
- Level: Undergraduate
- Language: English
- Subjects: Computer science, Engineering
- Source: [NPTEL](https://nptel.ac.in/courses/106108571)
- Licence: [CC BY-NC-SA](https://nptel.ac.in/faq) (Non-commercial use only.)
- Syllabus: [at the source](https://nptel.ac.in/courses/106108571)
- Who can watch: Tweens profiles and older (sources give no ratings; placed by Invisible Network from the source's own words)

## Lectures

1. [Lec 01 Course overview](https://invisiblenetwork.ai/learn/nptel/106108571/a9654559c042) (Video)
2. [Lec 02 Molecular biology and high-throughput sequencing](https://invisiblenetwork.ai/learn/nptel/106108571/6ec48779ccf7) (Video)
3. [Lec 03 Data structures/Algorithms Warmup](https://invisiblenetwork.ai/learn/nptel/106108571/eac1c846474c) (Video)
4. [Lec 04 Bitvector rank operations](https://invisiblenetwork.ai/learn/nptel/106108571/ffcd27002def) (Video)
5. [Lec 05 Demo for constructing rank data structure](https://invisiblenetwork.ai/learn/nptel/106108571/4272f11afabf) (Video)
6. [Lec 06 Z-algorithm](https://invisiblenetwork.ai/learn/nptel/106108571/eea7c5ef94d3) (Video)
7. [Lec 07 Suffix Arrays](https://invisiblenetwork.ai/learn/nptel/106108571/9dfb4baa36e1) (Video)
8. [Lec 08 Suffix array construction using prefix doubling](https://invisiblenetwork.ai/learn/nptel/106108571/0e5e0d8adc06) (Video)
9. [Lec 09 Demo for constructing suffix array](https://invisiblenetwork.ai/learn/nptel/106108571/5902d3311c34) (Video)
10. [Lec 10 Suffix Tree](https://invisiblenetwork.ai/learn/nptel/106108571/3b4dc9f13e81) (Video)
11. [Lec 11 Building Suffix Trees](https://invisiblenetwork.ai/learn/nptel/106108571/54fb7ab50457) (Video)
12. [Lec 12 Building Suffix Trees (Continued)](https://invisiblenetwork.ai/learn/nptel/106108571/34b7b74c7312) (Video)
13. [Lec 13 Applications of suffix trees](https://invisiblenetwork.ai/learn/nptel/106108571/16cd90182d24) (Video)
14. [Lec 14 Burrows Wheeler Indexes](https://invisiblenetwork.ai/learn/nptel/106108571/69c5abe9955d) (Video)
15. [Lec 15 Burrows Wheeler Indexes (continued)](https://invisiblenetwork.ai/learn/nptel/106108571/79b3a6b96da5) (Video)
16. [Lec 16 How is BWT useful for indexing genomes?](https://invisiblenetwork.ai/learn/nptel/106108571/75ed653345fa) (Video)
17. [Lec 17 Sequence Alignment and Edit Distance](https://invisiblenetwork.ai/learn/nptel/106108571/455a0c6e6870) (Video)
18. [Lec 18 Global and semi-global alignment](https://invisiblenetwork.ai/learn/nptel/106108571/20e34dee2ede) (Video)
19. [Lec 19 Local alignment](https://invisiblenetwork.ai/learn/nptel/106108571/0e35b81414b1) (Video)
20. [Lec 20 Scoring gaps in alignments](https://invisiblenetwork.ai/learn/nptel/106108571/301b218d82f9) (Video)
21. [Lec 21 Alignment significance statitstics](https://invisiblenetwork.ai/learn/nptel/106108571/a6db3b9845ed) (Video)
22. [Lec 22 Alignment demonstration](https://invisiblenetwork.ai/learn/nptel/106108571/4d67d3f3edbc) (Video)
23. [Lec 23 Heuristics for genome-scale alignment](https://invisiblenetwork.ai/learn/nptel/106108571/37935c883713) (Video)
24. [Lec 24 Maximal unique matches](https://invisiblenetwork.ai/learn/nptel/106108571/19c407ca57ca) (Video)
25. [Lec 25 Co-linear chaining](https://invisiblenetwork.ai/learn/nptel/106108571/54144c6c29b5) (Video)
26. [Lec 26 Incorporating gaps into the chaining algorithm](https://invisiblenetwork.ai/learn/nptel/106108571/16e562bf0f63) (Video)
27. [Lec 27 IGV Demonstration](https://invisiblenetwork.ai/learn/nptel/106108571/aea2825bd3f8) (Video)
28. [Lec 28 Genome assembly](https://invisiblenetwork.ai/learn/nptel/106108571/884b70d3f5c8) (Video)
29. [Lec 29 Shortest common superstring](https://invisiblenetwork.ai/learn/nptel/106108571/5c80567c0a14) (Video)
30. [Lec 30 Greedy algorithm for genome assembly](https://invisiblenetwork.ai/learn/nptel/106108571/d45bec299361) (Video)
31. [Lec 31 Genome assembly using de Bruijn graphs](https://invisiblenetwork.ai/learn/nptel/106108571/492684ccb25f) (Video)
32. [Lec 32 Multiplex de Bruijn graphs and Overlap graphs](https://invisiblenetwork.ai/learn/nptel/106108571/742eefc5a7f6) (Video)
33. [Lec 33 Assembly Demonstration](https://invisiblenetwork.ai/learn/nptel/106108571/49b523cb80f1) (Video)
34. [Lec 34 Introduction to phylogeny trees](https://invisiblenetwork.ai/learn/nptel/106108571/747427e3b32b) (Video)
35. [Lec 35 Distance based tree reconstruction](https://invisiblenetwork.ai/learn/nptel/106108571/5d5f9714db94) (Video)
36. [Lec 36 Character based tree reconstruction](https://invisiblenetwork.ai/learn/nptel/106108571/222baaff4e74) (Video)
37. [Lec 37 Phylogenetic trees Demo](https://invisiblenetwork.ai/learn/nptel/106108571/b95ddb4529c8) (Video)
38. [Lec 38 Hidden Markov Models](https://invisiblenetwork.ai/learn/nptel/106108571/329c66d16bd0) (Video)
39. [Lec 39 Hidden Markov Models (contd..)](https://invisiblenetwork.ai/learn/nptel/106108571/ba187395164a) (Video)
40. [Lec 40 ProtGPT2 Demo](https://invisiblenetwork.ai/learn/nptel/106108571/1340a70cddd2) (Video)
41. [Lec 41 Pangenome Graphs](https://invisiblenetwork.ai/learn/nptel/106108571/5a7a8d40bb16) (Video)
42. [Lec 42 Pangenome Demo](https://invisiblenetwork.ai/learn/nptel/106108571/8b7ca56c8cde) (Video)
43. [Lec 43 Multiple Sequence Alignment](https://invisiblenetwork.ai/learn/nptel/106108571/e79f2152ba50) (Video)
44. [Lec 44 Multiple Sequence Alignment Demo](https://invisiblenetwork.ai/learn/nptel/106108571/9c3dfd2378da) (Video)
45. [Lec 45 Sequence alignment to pangenome graphs](https://invisiblenetwork.ai/learn/nptel/106108571/42af64c1defe) (Video)
46. [Lec 46 Genomic Large Language Models](https://invisiblenetwork.ai/learn/nptel/106108571/f2bbf4e3e36c) (Video)
47. [Lec 47 Course Summary](https://invisiblenetwork.ai/learn/nptel/106108571/b64f1b52acca) (Video)
48. [Live Session 17-02-2025](https://invisiblenetwork.ai/learn/nptel/106108571/a9654559c042-2) (Video)
49. [Live Session 07-04-2025](https://invisiblenetwork.ai/learn/nptel/106108571/6ec48779ccf7-2) (Video)