Learn · Algorithms in Computational Biology and Sequence Analysis
Lecture 42 of 49Week 11 Pangenome Graphs
Lec 42 Pangenome Demo
Prof. Chirag Jain · IISc Bangalore
Credits and licence
- From
- Algorithms in Computational Biology and Sequence Analysis, IISc Bangalore (at NPTEL)
- Licence
- CC BY-NC-SA, as NPTEL states it. Non-commercial use only.
- Attribution
- NPTEL states: "Distributed under Creative Commons Attribution-ShareAlike / CC BY - NC - SA", beside a BY-NC-SA badge.
- Who can watch
- Tweens profiles and older. How courses are placed
All the lectures
- Lec 01 Course overview
- Lec 02 Molecular biology and high-throughput sequencing
- Lec 03 Data structures/Algorithms Warmup
- Lec 04 Bitvector rank operations
- Lec 05 Demo for constructing rank data structure
- Lec 06 Z-algorithm
- Lec 07 Suffix Arrays
- Lec 08 Suffix array construction using prefix doubling
- Lec 09 Demo for constructing suffix array
- Lec 10 Suffix Tree
- Lec 11 Building Suffix Trees
- Lec 12 Building Suffix Trees (Continued)
- Lec 13 Applications of suffix trees
- Lec 14 Burrows Wheeler Indexes
- Lec 15 Burrows Wheeler Indexes (continued)
- Lec 16 How is BWT useful for indexing genomes?
- Lec 17 Sequence Alignment and Edit Distance
- Lec 18 Global and semi-global alignment
- Lec 19 Local alignment
- Lec 20 Scoring gaps in alignments
- Lec 21 Alignment significance statitstics
- Lec 22 Alignment demonstration
- Lec 23 Heuristics for genome-scale alignment
- Lec 24 Maximal unique matches
- Lec 25 Co-linear chaining
- Lec 26 Incorporating gaps into the chaining algorithm
- Lec 27 IGV Demonstration
- Lec 28 Genome assembly
- Lec 29 Shortest common superstring
- Lec 30 Greedy algorithm for genome assembly
- Lec 31 Genome assembly using de Bruijn graphs
- Lec 32 Multiplex de Bruijn graphs and Overlap graphs
- Lec 33 Assembly Demonstration
- Lec 34 Introduction to phylogeny trees
- Lec 35 Distance based tree reconstruction
- Lec 36 Character based tree reconstruction
- Lec 37 Phylogenetic trees Demo
- Lec 38 Hidden Markov Models
- Lec 39 Hidden Markov Models (contd..)
- Lec 40 ProtGPT2 Demo
- Lec 41 Pangenome Graphs
- Lec 42 Pangenome Demo
- Lec 43 Multiple Sequence Alignment
- Lec 44 Multiple Sequence Alignment Demo
- Lec 45 Sequence alignment to pangenome graphs
- Lec 46 Genomic Large Language Models
- Lec 47 Course Summary
- Live Session 17-02-2025
- Live Session 07-04-2025