Bioinformatics I
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Contents |
Calendar
- Tuesday, September 16, 2008 (13:00-16:00): Literature presentation / Discuss practicals / Guided tour bioinformatics laboratory
- Tuesday, October 21, 2008 (13:00-16:00): Present and discuss results of genome analysis
Documents
Overview
Name course: Bioinformatics-I (Analysis and annotation of the human genome)
Course code: MINBI1-6
Credits: 6 ECTS
Period(s): Semester 1 block 1 (september/october 2008)
Educational Institute: Master School of Informatics
Lecturer(s): Prof. dr. Antoine HC van Kampen, Barbera DC van Schaik
Is part of: Master Computational Science
Objectives:
Learn the basic principles of analyzing and annotating the human genome
Contents:
During the course the students will:
- analyze the composition of the human genome
- determine the location of protein coding genes (and their structure)
- determine the location of non protein coding genes (RNA genes)
- examine the organization of repetitive DNA
- search for commonalities and differences between the above elements
The students will develop their own software to analyze the human genome.
Recommended prior Knowledge: programming (e.g. Perl), basic knowledge molecular biology
Format:
- Literature study
- Lectures
- Computer practicals
Study materials:
- Relevant literature will be handed out at the start of the module
- Book: Tisdall, JD (2002) Beginning Perl for Bioinformatics, O'Reilly Media, Sebastopol
Assessment:
The grade for this module will be based on a literature presentation and on the report containing the results of the above mentioned analyses.
Literature study
We will prepare for the use case of this module. To get insight into genome assembly and annotation of genes the following papers are studied. Each course member will give a literature talk on September 15, 2008 (~30 minutes) about one of these papers/subjects:
- Lander et al (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860. (pdf) Page 875-892, from "Broad genomic landscape" till "Gene content of the human genome".
- Next generation sequencing:
- Guigo et al (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology, 7 (Suppl I):S2 (pdf)
- Gerstein et al (2007) What is a gene, post-ENCODE? History and updated definition. Genome Research, 17, 669 (pdf)
- Meyer (2007) A practical guide to the art of RNA gene prediction. Briefings in Bioinformatics, 8(6), 396. (pdf)
Case study: comparison of protein-coding and non-coding genes
Not all genes code for proteins. There is a group of genes where the transcribed RNA molecule is functional. In this case study we will analyse the sequence properties of protein-coding and non-coding genes and check whether there are differences. E.g. is there a difference in nucleotide composition between these types of genes? Can you predict the type of gene based on di-, tri-, etc combinations of nucleotides? Are regions of the genome that do not consist of genes junk?
