27611 Introduction to Bioinformatics
|Introduktion til bioinformatik|
Point( ECTS )
Taught under open university
|Technological specialization course, MSc. Eng., Bioinformatics Systems Biology|
|F4A (tues 13-17)
Scope and form:
|Lectures and computer exercises|
Duration of Course:
|F4A, Decide with teacher|
Type of assessment:
Not applicable together with:
General course objectives:
Students should become familiar with the use of computers for
molecular structure and sequence analysis, with special emphasis on
applications in microbiology, biotechnology and biotech industry.
Introduction to Bioinformatics is a practically oriented course
with focus on the practical use of the methods. A large part of the
course is computer-based exercises.
A student who has met the objectives of the course will be able to:
- Explain how the information in biological macro-molecules, such
as DNA and protein can be represented in an electronical
- Explain how DNA and protein sequences from related organisms
are influenced by a common evolutionary history.
- Search for sequence and structure data from the publicly
available databases, such as GenBank, UniProt and PDB.
- Visualize protein 3D structure using computer software.
- Generate and critically evaluate DNA and peptide
- Query sequence databases using alignment based methods (BLAST)
and critically evaluate the results
- Predict the most probable biological function of a novel gene
or protein product by comparison to already characterized
- Generate multiple sequence alignments of sets of related
sequences – using both globally and locally optimized
- Generate phylogenetic trees from multiple alignments.
- Generate and interpret visualizations of the information
content of sets of related sequences (“logo
Evolution at the DNA level. Taxonomy. Practical use of taxonomy
Biological information. Information content in biological
macro-molecules. DNA sequencing – including error sources. DNA
sequences in electronical format. How to use the GenBank database.
Protein sequences. Protein structure levels. Protein sequences in
electronical format. Sources of protein sequences (direct
sequencing and computer based translation). How to use the UniProt
Protein structure. How protein structures are determined. Quality
of protein structure data. How to use the PDB database. Computer
based visualization of protein structure.
Pairwise alignment. Alignment scores, gaps, substitution matrices.
Global and local alignment.
BLAST. How to use BLAST for searching sequence databases. Critical
evaluation of results. Iterative BLAST.
Multiple alignments. The use of heuristic methods due to data
complexity. Globally and locally optimizing algorithms.
Generation and interpretation of phylogenetic trees from multiple
alignments. The NJ algorithm for tree construction. Rooted versus
Weight-matrix based methods. How to search using weight-matrices.
Generation and interpretation of LOGO plots.
Lecture notes and exercise manuals handed out during the
Green challenge participation:
Please contact the teacher for information on whether this course
gives the student the opportunity to prepare a project that may
participate in DTU´s Study Conference on sustainability, climate
technology, and the environment (GRØN DYST). More infor
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Last updated: 04. juni, 2014