Bioinformatics
Lecture notes :
- link to download: Complete lecture slides (slides only , no video) (large file: 180 Mb)
To facilitate the comprehension, the videos will follow closely the slide content; lectures are partitioned in 15-20 minute videos.
Implementations: short programs useful to check data structures, loops, etc (not examinable); Note below could be useful for further detailsWIP means work in
progress
Weekly availability to meet
students and
supervisors (send email to pl219). I am happy to send more
materials
on some topics (without changing the level of difficulty of exam
questions).
- Lecture1 (Video): Introduction and Biological concepts (NON EXAMINABLE) (large file: 10 Mb)
- Data
Repositories (with link to human reference genome)
- Genome sequence of Sars-cov2 (NC_045512.2)_ non examinable
- Biopython (tutorial)- non examinable
- Lecture1 (Video): Longest common subsequence (large file: 10 Mb)
- Lecture2 (Video): Global and Local alignment (large file: 10 Mb)
- Lecture2 (Video): Linear Time alignment (Hirschberg) (large file: 10 Mb)
- Lecture2 : Four Russians speedup; RNA folding (large file: 10 Mb)
- Lecture3 (Video): Building trees (large file: 10 Mb)
- Lecture3 (Video): Additive Phylogeny (large file: 10 Mb)
- Lecture3 (Video): UPGMA and Neighbor-Joining (large file: 10 Mb)
- Lecture3 (Video): Small and Large Parsimony ; trees and multialignment(large file:10 Mb)
- Lecture4 (Video): Genome Sequencing (large file: 10 Mb)
- (Video): DeBruijn Graph (large file: 10 Mb)
- Lecture4 (Video): DeBruijn Pairs (large file: 10 Mb)
- Lecture5 (Video): Lloyd algorithm for clustering (large file: 10 Mb)
- Lecture5 (Video): Expectation-Maximisation (large file: 10 Mb)
- Lecture5 (Video): Markov Clustering Algorithm (large file: 10 Mb)
- Lecture6 (Video): Genome Assemble (large file: 10 Mb)
- Lecture6 (Video): Burrows-Wheeler Transform (large file: 10 Mb)
- Lecture7 (Video): Hidden Markov Models: Viterbi (large file: 10 Mb)
- Lecture7 (Video): Hidden Markov Models: Forward and Backward (large file: 10 Mb)
-
- Implementation: Forward and Backward.py
- Implementation: TMHMM.py Transmembrane protein segments prediction
- Lecture8 (Video): How to compute with DNA (large file: 10 Mb)
- Lecture9 (Video): How to use DNA as memory storage (large file: 10 Mb)
- Lecture10 (Video): How to simulate genetic and protein reaction networks: Doob-Gillespie (large file: 17 Mb)
- Lecture 11 Revision
(Video)
,
Textbook reference
,
Revision note 1
,
Revision note 2
,
Revision note 3
(large
files:
10 Mb)
- Lecture12 (Video): Example Class (I am happy to organise online example class with students) (large file: 10 Mb) Link to Bioinformatics Example class slides only
- Additional References: original papers (PDF) (non necessary for the exams!)