BOX: experimental bioinformatics (M1)
The purpose of this module is to give an overview of bioinformatics to students with a theoretical CS background, introducing them to data-driven reasoning, practical algorithmics and making them reason on poorly formalized problems.
- Genome assembly
- Pattern matching
- Tutorial (Burrows-Wheeler transform)
ALG: algorithms for bioinformatics (M2)
The purpose of this module is to give bioinformaticians insights on the building blocks behind main bioinformatics tools. I personally focus on exact pattern matching with string preprocessing.
- Lectures notes (draft)
Tutorial 1 (suffix tries)
Additional files: template.py, genome1.fa, genome2.fa.Tutorial 2 (dynamic programing)
Additional files: template.py, genomes.fasta.Tutorial 3 (Burrows-Wheeler transform and FM-index)
Additional files: template.py, karkkainen_sanders.py, hiv1.fa, dudh.txt.
BIF: Bioinformatics (M1)
The purpose of this module is to give computer scientists the opportunity to discover (some of) the algorithms and data structures used in bioinformatics. I personally focus on exact pattern matching with string preprocessing.
-
Tutorial 1 (suffix tries and trees)
Additional files: template.py, genome1.fa, genome2.fa.
Correction: correction.py. -
Tutorial 2 (Burrows-Wheeler transform and FM-index)
Additional files: template.py, dickens.txt, dudh.txt, random.txt.