BIF-30806 Advanced Bioinformatics


Credits 6.00

Teaching methodContact hours
Literature study8
Practical intensively supervised72
Course coordinator(s)(postuum)prof. dr JAM Leunissen
Lecturer(s)(postuum)prof. dr JAM Leunissen
dr. ing. H Nijveen
Examiner(s)(postuum)prof. dr JAM Leunissen

Language of instruction:


Assumed knowledge on:

MIB-21306 Bioinformation Technology

Continuation courses:



The course is divided into 5 modules and a short bioinformatics research project.
1. Bioinformatics script programming in Perl. Perl is the most popular programming language used in bioinformatics to perform automated tasks ranging from simple repetitive tasks to complex data analysis.
2. The students will become familiarized with the advanced use of the SRS data retrieval system and other systems for automated batch processing of primary and secondary databases such as genomics (Ensembl), genetics (OMIM), structural (pFam), pathway (KEGG) and ontology (GO) databases.
3. Advanced database-searching techniques and sequence comparison methods.
4. Introduction to text mining, and the importance of natural language processing (NLP), thesauri and ontologies in text and database searching.
5. Design and implementation of bioinformatics analysis pipelines, using workflow management tools (Taverna) and web services (SOAP, BioMOBY)

Learning outcomes:

- applying and automating advanced batch-wise sequence searching and retrieval techniques, specifically BLAT, BLAST and SRS;
- Perl programming and Perl library development;
- design and implementation of a bioinformatics analysis pipeline;
- development of web services using BioMOBY;
- cooperative modular software design;
- integrative bioinformatics;
- detailed understanding of sequence analysis algorithms;
- basic knowledge of data mining techniques, specifically knowledge of Bioconductor/R for microarray analyses;
- an understanding of text mining techniques;
- methods in sequence function assignment such as orthology and clustering techniques;
- Perl language and the BioPerl and GD libraries;
- workflow management using web services specifically SOAP, BioMOBY and Taverna.


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


Written reports on the results obtained with the exercises (30%), a written report on the research project (50%) and an oral presentation of the research project (20%).


Book: James Tisdall "Mastering Perl for Bioinformatics", ISBN: 0-596-00307-2 (optional). Other literature and exercises are made available in electronic form during the course.

Restricted Optional for: MPBPlant BiotechnologyMScC: Molecular Plant Breeding and Pathology4WD