SSB-20306 Bioinformation Technology


Vak code vorig jaar: (MIB-21306)

Vak

Studiepunten 6.00

OnderwijstypeContacturen
Lectures12
Practical intensively supervised105
Self-study
Course coordinator(s)dr. PJ Schaap
Lecturer(s)dr. PJ Schaap
prof. dr. SC de Vries
prof. dr. D Weijers
dr. ir. JE Wellink
dr. ir. JJM Vervoort
Examiner(s)dr. PJ Schaap
dr. HGJM Franssen
prof. dr. SC de Vries
dr. ir. JJM Vervoort

Language of instruction:

English

Assumed knowledge on:

Cell Biology I, Microbiology & Biochemistry or Gentechnology

Continuation courses:

Genomics and Applied Bioinformatics

Contents:

The course is divided in 8 modules:
1. An introduction in DNA sequence analysis. In this module it is explained what we can and what we can not do with a primary DNA sequence analysis.
2. An introduction in computational proteomics: A primer on high-throughput tandem mass spectrometry of peptides and proteins. An overview of its applications is given, demonstrating the use of LC-MS-MS data in identifying proteins of interest.
3. Sequence alignments and (sequence) database queries. An introduction to text-mining tools, matrices and the FastA and Blast sequence comparison methods. Topics include sequence search strategies, the dynamic algorithms involved, matrix derived raw-scores, Bit-scores and E-values.
4. An introduction in transcriptome analysis. Topics are the construction of arrays, their usage and limitations. Real array data will be used to demonstrate how these data can be applied in solving biological questions.
5. Usage of specialised Internet sites for extracting topological signals from protein sequences.
6. Multiple sequence alignments as a tool to clarify the function(s) of an unknown protein, to aid in cloning of a gene and to extract phylogenetic signals. Assumptions, limitations and pitfalls are discussed.
7. Annotation of DNA and protein sequences and Ontologies.
8. Protein models and structures. Comparison of three-dimensional protein structures and usage of structural databases, like CATH, SCOP, FSSP and MMDB. Homology based three-dimensional modelling of proteins.

Learning outcomes:

Intended learning outcomes:
Knowledge:
- widely used bioinformatics applications for DNA assembly, translation into proteins, sequence alignments, identification of protein motifs and protein structure prediction;
- advantages and shortcomings of databases that store text, nucleotide and protein sequences and DNA microarray data;
- advantages and shortcomings of DNA and protein sequence analysis software using FastA or BLAST algorithms and in use for multiple sequence alignment, SRS, topological signal prediction, protein 3D prediction;
- an understanding of the appropriate application of a range of bioinformatics software.
Skills:
- a familiarity with the use of much of the existing software for the analysis of DNA and protein data;
- an ability to select the most appropriate bioinformatics tools for a given analysis;
- an ability to synthesise genomics information with respect to the biological questions.

Activities:

Hands on course introductory lectures, training and study of relevant literature.

Examination:

Reading and discussion of papers (10%) a theoretical exam (45%) and an assignment (45%). The results of the 2-day assignment will be presented in the form of a written report combined with an oral presentation.

Literature:

Book: Bioinformatics (Methods express) ISBN: 9781904842163. Lectures additional reading and hands-on excercises are made available in electronic form (Black Board) during the course.

OpleidingFaseSpecialisatiePeriode
Verplicht voor: BBIBiologyBScA: Cell and Molecular Biology5MO
BPWPlant SciencesBScA: Plant Genomics and Health5MO
Keuze voor: BBTBiotechnologyBSc1MO, 5MO
MBTBiotechnologyMScA: Cellular/Molecular Biotechnology1MO, 5MO
MBTBiotechnologyMScB: Food Biotechnology1MO
MBTBiotechnologyMScC: Medical Biotechnology1MO
MBTBiotechnologyMScF: Marine Biotechnology1MO, 5MO
MBTBiotechnologyMScE: Environmental and Biobased Biotechnology1MO, 5MO
MMLMolecular Life SciencesMScA: Biomedical Research1MO, 5MO
MMLMolecular Life SciencesMScB: Biological Chemistry1MO, 5MO
MNHNutrition and HealthMScC: Molecular Nutrition and Toxicology1MO, 5MO
MBFBioinformaticsMSc1MO, 5MO
MinorPeriode
Keuze voor: WUSYBBSc Minor Systems Biology1MO