Bioinformation Technology -1 Winner of the Netherlands Biotechnological Society (NBV) biannual Biotechnology prize "Zilveren Zandloper 2000". 8 - 16 November, 2004 Wageningen, The Netherlands A 7-day hands-on course in applied bioinformatics. Students are provided with a syllabus, exercises and some additional bioinformatics tools. |
Course prerequisites
Basic background knowledge in Cell Biology, Molecular Biology and Genetics is required. Without these courses (and even if you had these courses), it is anticipated that students will need to carry out review and remedial work for the following topics: cell biology, molecular biology, recombinant DNA technology, and protein structure/function. No programming skills or significant mathematics background will
be necessary for this course. Some experience with computers, email, and navigating the Internet however is necessary.
Course aim
The general objective of the course is to provide in seven days an introduction to and overview of the fields of bioinformatics. As an introductory course, the focus will not be on the theoretical and computational aspects of the fields. The aim is to provide a practical description of the topics, tools,
issues and current trends in the fields including their impact on biology, biotechnology, agriculture, human health and medicine.
Course design
The course is divided in 7 modules. A summary of each module is given below.
Modules
Monday November 8, Module 1:
Basic DNA-handling.
In this module it is explained what we can and what we can not do with sequence analysis. Furthermore, a small and a large genome project is discussed. In the exercises a contig is build from raw DNA sequences.
By using peptide sequences an open reading frame is localised in a large genomic DNA fragment by means of simple Perl scripts. The exercises also demonstrate the various strategies that can be applied to achieve these goals.
Tuesday November 9, Module 2:
Proteomics:
We will give an overview of the different techniques that can be used to generate proteomics data. In the exercises we will handle 2D gels, MS and MS/MS to determine protein function and posttranslational modifications. In addition, we will discuss the different methods to identify protein-protein interactions (yeast 2-hybrid, MS + affinity chromatography and in silico techniques).
Wednesday November 10, Module 3:
Sequence alignments and database queries.
The module consists of two parts. In the first part matrices are introduced. Discussed are the Dayhoff mutation data matrix, the BLOSUM series of matrices and matrices derived from tertiary structure alignments. Also is discussed when to use which matrix. Part 2 introduces the FastA and Blast sequence comparison methods. Topics are sequence data pre-processing, principles of the dynamic algorithms involved, E- and init-values, Bit-, Z- and Opt-scores and output parsing. The exercises demonstrate
the differences between the FASTA and BLAST algorithms and demonstrate the effects of user-defined settings. PSI and PHI profile blasts and motif searches are also demonstrated.
Thursday November 11, Module 4:
Topological signal detection.
There are a number of specialised algorithms that can help you to make an educated guess on the function and whereabouts of an unknown protein. In the exercise websites are visited that can identify various putative topological signals within amino acid sequences. We will also use a local algorithm that can predict topological signals using a multiple protein file as input.
Friday November 12, Module 5:
Transcriptomics I
A brief introduction in the various techniques used to produce transcriptome data, with emphasis on microarrays. The focus will be on dealing with sources of technical and biological variation in data generation (pre-processing, normalisation and experimental design). In addition, we will explain the principles of different statistical and non-statistical approaches in transcriptomics data analysis linked to their visualisation techniques (t-test, ANOVA, PCA, fold change, clustering).
Monday November 15, Module 6:
Transcriptomics II
Continuation of the principles of different approaches in transcriptomics data analysis. By combining transcriptomics data with for example genome analysis (transcription factor binding sites) more information about gene regulation/function can be obtained. These techniques will be exercised using a yeast diauxic shift microarray experiment.
Tuesday November 16 Module 7:
Multiple sequence alignments
A multiple sequence alignment can be used to transfer knowledge from a known protein to an uncharacterised protein. We will demonstrate how knowledge can be transferred to be used as an aid to in a method to clone a certain gene from your favourite organism or as an aid to extract phylogenetic signals. We will discuss
assumptions and limitations in multiple alignment and the COG database. In the exercise we will practice multiple sequence alignments using clustalX and learn how to display the obtained results in the form of a (un)-rooted tree.
Course coordinator
Peter Schaap
E-mail Peter.Schaap@wur.nl
Lecturers
Dr. P. Schaap
Dr. I. Rienties
Dr. J. Vervoort
Prof. Dr. S. de Vries
Dr. C. Maliepaard
Study load
The study load of this course is 2.0 ECTS credits.
Location
Building: Transitorium
Address: Deijenlaan 3, Wageningen
Room: K2043
We have 38 seats in total. The course is primarily meant for PhD students from the graduate school VLAG. There will be no selection procedure in advance, see however course prerequisites
€ 100,- VLAG PhD students
€ 400,- PhD students
Euro 400,- WUR Employees
Euro 1600,- Other participants
Registration: Please send an E-mail to vlag@wur.nl. Indicate research school and category (PhD/Employee/Other). Selection will be done on the basis of: "First in first served"
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