Module: Theory of Bioinformatics 1

* depending on the student population

Learning outcomes (leerdoelen)

You will learn about the following concepts and techniques, and how to apply them to real-life datasets and problems:

• The uses of Next GenerationSequencing (NGS) in modern experimental design
• Next Generation Sequencers: Illumina HiSeq, PacBio, MinION; how they work and the data they generate
• Protein structure & feature conservation
• Alignment of 2 sequences using ClustalO and an appreciation of the underlying concept; use via the EBI website
• Fast alignment of NGS data: mappers such as bowtie2 and BWA: how they work conceptually and how they can be used from Galaxy
• Downstream analysis of NGS alignment/mapping results; file types and pipelines in Galaxy
• SNP and indel calling in alignment data; statistics, software and embedding in Galaxy

Contents

Bioinformatics is built on two great assumptions: that evolutionary relationships between proteins will show up in the DNA sequence coding for them, and that you can use these relationships in bulk to predict the likelihood that any 2 or more novel sequences are related. These two assumptions allow you to create alignments between wildly different DNA and protein sequences which allow you to compare them base by base or amino-acid by amino-acid with statistical confidence. From these alignments you can then infer whether mutations have occurred which affect the function of the protein in some way. Because Next Generation Sequencing produces such large amounts of data, new alignment methods have been developed which trade accuracy for speed. This course will introduce both the theory and practice of sequence alignment for inferring function, aligning reads from NGS and using these alignments to draw biological conclusions.

Literature and other resources

Literature

• Introduction to Bioinformatics 4th Edition. ISBN-13:978-0199651566

Web

• Blackboard course of the minor

Competences

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Method

• lecture

Entry demands

• You need to be enrolled in a Bachelor programme in the Domain of Applied Science.

Entry demands for test

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Foreknowledge

• We assume knowledge of the central dogma of biology

Foreknowledge can be obtained through

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Resources for self study

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Mandatory materials

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Recommended materials

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