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27622 Introduction to Bioinformatics - Turbo version

27622 is a MSc level turbo version of the full semester Introduction to Bioinformatics course (27611). The first part of this course involves lectures and exercises with the same curriculum as 27611. The second part of the course consists of group project work.

Danish title:

Introduktion til bioinformatik - turbo version

Language:


Point( ECTS )


5

Course type:

MSc
Taught under open university

Schedule:

June
The course will be closed and not offered in June 2014.
 

Location:

Campus Lyngby

Scope and form:

Lectures and computer exercises with project work in the last week of the course.

Duration of Course:

3 weeks

Date of examination:

Decide with teacher

Type of assessment:

Aid:

Evaluation:

Not applicable together with:

Qualified Prerequisites:

,

Participants restrictions:

Minimum 10 Maximum: 40

General course objectives:

Students should become familiar with basic computer-based methods for molecular structure and sequence analysis. The theory behind the methods is presented, but the main focus is on the practical application of the methods towards a problem-based research project.

Learning objectives:

A student who has met the objectives of the course will be able to:
  • Search for sequence and structure data from the publicly available databases, such as GenBank, UniProt and PDB.
  • Visualize protein 3D structure using PyMOL.
  • Generate and critically evaluate DNA and peptide alignments.
  • Visualize genomic data using the UCSC Genome Browser.
  • Predict epitope binding affinity using web-based tools.
  • 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 genes/proteins.
  • Generate multiple sequence alignments of sets of related sequences – using both globally and locally optimized algorithms.
  • Generate phylogenetic trees from multiple alignments.
  • Generate logo plots to represent sequence conservation.
  • Execute a bioinformatics-based group research project involving multiple analytical modalities, and present the results orally and in a poster.

Content:

Evolution at the DNA level. Taxonomy. Practical use of taxonomy databases.

Biological information. Information content in biological macro-molecules. DNA sequencing – including error sources. DNA sequences in electronic format. How to use the GenBank database.

Protein sequences. Protein sequences in electronic format. Sources of protein sequences (direct sequencing and computer based translation). How to use the UniProt database.

Protein structure. Protein structure levels. How protein structures are determined. Quality of protein structure data. How to use the PDB database. Computer-based visualization of protein structure using PyMOL.

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 unrooted trees.

Weight matrix based methods. How to search using weight matrices. Generation and interpretation of logo plots.

Immunological bioinformatics. Sequence-based methods in bioinformatics. Epitope prediction and vaccine development.

Remarks:

Course literature:
Lecture notes and exercise manuals handed out during the course

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 http://www.groendyst.dtu.dk/english/Conference/Practical-info/Start-up

Department:

27 Department of Systems Biology

Home page:

http://www.cbs.dtu.dk/courses.php

Registration Sign up:

At CampusNet
Last updated: 05. november, 2013