NWI-MOL073
Comparative Genomics
Course infoSchedule
Course moduleNWI-MOL073
Credits (ECTS)3
CategoryBA (Bachelor)
Language of instructionEnglish
Offered byRadboud University; Faculty of Science; Moleculaire Wetenschappen;
Lecturer(s)
Coordinator
prof. dr. M.A. Huijnen
Other course modules lecturer
Lecturer
prof. dr. M.A. Huijnen
Other course modules lecturer
Contactperson for the course
prof. dr. M.A. Huijnen
Other course modules lecturer
Examiner
prof. dr. M.A. Huijnen
Other course modules lecturer
Academic year2022
Period
KW3  (30/01/2023 to 09/04/2023)
Starting block
KW3
Course mode
full-time
RemarksMax. no. of participants: 30.
Open for university students Biology and MLS. Succes rate of HBO-minor students is low.
Registration using OSIRISYes
Course open to students from other facultiesNo
Pre-registrationNo
Waiting listYes
Placement procedureDone manually by Back Office
ExplanationDone manually by Back Office
Aims
At the end of the course the student is able to:
  • detect homology between sequences using multiple techniques, ranging from pairwise sequence comparisons to comparisons at the level of sequence profiles.
  • make a Hidden Markov Model of a sequence alignment and understand this process.
  • derive phylogenies and interpret their results in the context what is known about the sequences and the species they come from.
  • predict RNA secundary structures and use pattern recognition techniques on DNA sequences.
  • compare genomes at the level of shared orthologous genes and interpret the results.
  • predict function relationships between proteins using genomics data and their integration using Bayesian methodology.
  • explain the theories about metabolic pathway evolution and how they can be tested using sequence data.
Content
The topic of this course is how to convert genomic sequence data and other types of genomics data into biological knowledge and understanding. Sequence analysis and prediction of protein function are performed on multiple levels, ranging from comparing two protein sequences, to the prediction of their function by comparing multiple genomes and the analysis of the topology of protein interaction networks.
The course starts with the elementary steps of sequence analysis, including gene prediction (which DNA encodes proteins or RNA), sequence comparison (how do we know two sequences are homologous and what is the best method to determine sequence homology), and RNA structure prediction (e.g. how do we predict miRNAs).
After covering the most elemental steps and their applications, we will move to the analysis of complete genomes and their comparison. Here we will show how one can predict which pathways are encoded in a genome, and also how genomes can be used to predict new pathways. Furthermore we cover aspects of systems biology directly related to genomics data. How can we integrate genomics data to obtain reliable predictions about e.g. the function of a protein, how can genomics data represented as networks and how to analyze such networks. As molecular sequences are a direct result of evolution the course also teaches how to use evolutionary information in the analysis of sequence data, and how to separate the effects of selection from those resulting from mutation pressures.

Instructional Modes
Level

Presumed foreknowledge
Bioinformatics knowledge, i.e. the course Bioinformatica A (NWI-MOL075) or a background in Biochemistry. The course is aimed at university students of Molecular Life Sciences and Medical Biology. Success rate of HBO-minor students and premaster students has proven to be low. This is a course in the programme 'Molecular Life Sciences'.
Test information
Written exam. All students give a presentation on one of the assignments they have made. This presentation is part of the grading.
Specifics

Required materials
Handouts
Powerpoint presentations and assignments are available on blackboard

Instructional modes
Lecture

Practical computer training
Attendance MandatoryYes

Tests
Exam
Test weight1
Test typeExam
OpportunitiesBlock KW3, Block KW4

Remark
Final grade based on exam and assignment.