Introduction to Bioinformatics

URL study guide

https://studiegids.vu.nl/en/courses/2024-2025/X_401036

Course Objective

We can now routinely sequence the DNA of a human genome or map which genes are expressed when, but do we actually understand how these genes work, form a living organism together, and what can go wrong? Bioinformatics focuses on the question of what the biological meaning and function of DNA (and protein) sequences is, and tries to give answers using computational techniques. During this course, students get an overview of the most important topics/techniques within bioinformatics. In particular, the focus is on the fields of genomics and transcriptomics. Practical skills students will master at the end of this course are:
- Independently searching for homologous (related) sequences of a DNA fragment in a large sequence database, using the BLAST algorithm. Special attention is given to a variant of this algorithm: PSI-BLAST.
- Being able to interpret the results of a gene expression using plots made with the statistical program R. Furthermore, students also develop collaboration skills, because they have to work on assignments in pairs.

Course Content

The following topics are covered: Theory:
- Genomics, sequence databases and the search for homologues in a database
- Pairwise sequence alignment (Dynamic programming algorithms)
- PSI-BLAST, evolutionary profiles and protein structures
- Gene expression analysis
- Machine learning methods Practical assignments:
- Sequence database search: how to search for homologous sequences of proteins or DNA with the BLAST program.
- Gene expression: how to interpret the results of a gene expression analysis.

Teaching Methods

11 meetings, consisting of 6 lectures, 4 practicals and a question hour for the exam.

Method of Assessment

Written exam (50%) and two practical assignments (20% and 30%).

Target Audience

2MNW, 3F, 3S, 3-SBI, mBio, mi-Sc, mi-BI

Additional Information

Mandatory for 2MNW students. Third year Bachelor student in any beta or life science discipline (including Medicine) are allowed to enter.

Entry Requirements

Basic knowledge of molecular biology and statistics.