Masters Course: Introduction to Bioinformatics for Molecular Biologists

AIM: To introduce commonly used bioinformatic concepts, tools and resources in molecular biological research.

Date: 12-11-2012 till 23-11-2012 (2 weeks full time, 3 ECTS), Venue Stratenum str. 2.106 / 2.112

Description: “Introduction to Bioinformatics for Molecular Biologists” is a joint course for the various life science Masters programs at the Utrecht University. This introductory course provides an overview of the importance of bioinformatics in various biological disciplines. While a biological background is required, no programming skills are needed. The course can be considered a general introduction to bioinformatics, with a focus on the research that is performed at Utrecht University. The theory and tools for bioinformatics provided are very useful for any life science researcher. The course will be partially theoretical with lectures taking up to 30% of the day while the major focus will be on working with various tools and datasets. These computer tasks are performed in groups of 2 students. The maximum number of participants for this course is 40 students. The course will be concluded on the last day with an exam that consists of normal pen-and-paper questions but also of tasks that should be completed on the computer. Active participation during the course provides sufficient preparation to complete the exam. Furthermore, follow-up courses are organized later in the year that will allow you to specialize in specific directions. Students are expected to be familiar with the subjects from this introductory course when participating in any of the follow-up courses.

Course coordinator: Berend Snel,,030-253 8102


The maximum number of participants for this course is 40 students.

Part 1: Exploration of Genomes Coordinator Van den Ackerveken

To understand how genome sequences are generated, annotated and can be accessed and browsed

To understand and work with Ensembl, and NCBI genome browsers

To understand genomic contents, e.g. protein coding genes, regulatory elements, non-coding genes, alternative introns, UTRs

To understand that there is variation in sequences within populations and how this affects the phenotype and disease. (genetic variation/SNP/disease/ phenotypes)

Monday 9:00-16:30

Genome Sequencing

Lecture Genome Sequencing

Lecture Introduction to similarity searching

Hands-on Sequence assembly and annotation

Lecture Ensembl Genome browser

Hands-on Ensembl Genome browser

Tuesday 9:00-16:30

Exploring the Genome

Lecture Next Generation Sequencing (NGS)

Hands-on exersise: Working with NGS data

Lecture: Genome mining tools

Hands-on Biomart

Lecture Genome Variation

Hands on SNPs, haplotypes and CNVs

Wednesday 9:00-14:30

Genome Variations and their Relevance to Human Traits and Diseases

Lecture: Mapping disease genes

Hands-on exercises: Linkage and association

Lecture Next Generation Sequencing Applications

Lecture Personal Genomics

Hands-on exercise Personal genomics

Wednesday 14:30-17:00

Self study

Part 2: Protein sequence and structure analysis Coordinator Snel

To understand sequence comparison methods and to use them in DNA and protein analysis

To learn to use tools to predict the three dimensional protein structure based on the primary sequences

To understand the relationship between sequence conservation and structure and function

To be able to construct and interpret a phylogenetic tree of genes or proteins in terms of gene duplications and orthology.

Thursday 9:00-15:00

Using sequence analysis to find homologs

Lecture pairwise alignment

Hands-on pairwise alignment

Lecture sequence database searching

Hands-on sequence database searching

Lecture profile searches

Hands-on profile searches

Friday 9:00-16:30

Structure-function relationships of proteins Lecture: From primary sequence information to tertiary protein structure

Hands-on: Structure predictions based on protein sequences

Lecture: Homology modeling

Hands-on/demo: structure viewers JMOL and Deep-View (Swiss-PDB viewer)

Hands-on: Homology modeling

Lecture Structure-Function relationship

Hands-on: Functional annotation through structural similarity

Monday 9:00-14:30

Phylogeny and comparative genomics

Lecture: Construction and primary interpretation of phylogenetic tree

Hands-on exercise Construction and primary interpretation of phylogenetic trees

Lecture: interpretation of phylogenetic trees

Hands-on exercise: interpretation of phylogenetic trees

Lecture: genome duplications

hands-on exercise: genome duplications

Monday 14:30-17:00

Self study

Part 3: Systems Biology Coordinator Lijnzaad

To learn the basics of a number of high through-put quantitative experiments and their analysis, in particular microarrays and protein mass-spectrometry. This requires the use of statistics and multivariate analysis methods such as clustering, which are also introduced.

To know how to bioinformatically interrogate functional networks of interactions between genes and proteins as obtained from high-throughput experiments of protein-protein interactions and protein-DNA interactions.

Tuesday 9:00-16:30


Introduction to microarrays

Introduction to microarray statistics


Gene Ontology

Wednesday 9:00-16:30


Lecture Introduction proteomics

Hands-on Mass Spectrometry Finger Printing (MS-FP)

Lecture(s) Tandem Mass Spectrometry

Hands-on Tandem Mass Spectrometry (MS/MS)

Lecture De Novo Peptide sequencing

ands-on De Novo sequencing (optional)

Lecture Applications in proteomics

Hands-on using NetworKIN

Thursday 9:00-14:30


Lecture Interactome networks

Hands-on Interactome networks

Lecture 'From Tandem Affinity Purification (TAP) to protein complexes'

Hands-on 'From Tandem Affinity Purification (TAP) to protein complexes'

Lecture Complementary Data integration

Hands-on Complementary Data integration

Thursday 9:00-14:30

Self study

Exam and Question Hour

Friday 12:00-12:30

questions regarding the topics and tasks that were covered during the week

Friday 13:00-16:00

Exam:OPEN BOOK, pen&paper and PC-exercises


dr. Berend Snel ( Department of Biology, Faculty of Science

dr. Guido Van den Ackerveken ( Department of Biology, Faculty of Science

dr. Bas van Breukelen ( Department of Pharmaceutical Sciences, Faculty of Science

dr. Gert Folkers ( Department of Chemistry, Faculty of Science

dr. Philip Lijnzaad ( Molecular Cancer Research, University Medical Center Utrecht

dr. Patrick Kemmeren ( Molecular Cancer Research, University Medical Center Utrecht

dr. Carolien de Kovel ( Department of Medical Genetics, University Medical Center Utrecht

dr. Ies Nijman ( Hubrecht Institute, University Medical Center Utrecht