Introduction to Bioinformatics

Computational analysis of biological data using R programming. Students learn to analyze DNA sequences, discover genes, and understand biological patterns through hands-on programming. The course bridges biology and computer science, teaching practical skills for modern biomedical research.

Students work with real gene sequences from public databases, learning GC content analysis, sequence comparison using dot plots, codon frequency analysis, and automated gene finding algorithms. The course progresses from basic R programming to specialized bioinformatics libraries for DNA analysis.

Assessment includes computer-based practical tests requiring live coding and analysis with R using biological datasets, ensuring students can apply computational methods to real research problems.

Interactive Final Exam - Computer-based examination testing practical bioinformatics skills

1 Sources

The content of this course is based on A Little Book of R for Bioinformatics by Avril Coghlan and A Little Book of R for Bioinformatics 2.0, by Avril Coghlan, with contributions by Nathan L. Brouwer. They have a Creative Commons Attribution 3.0 License.

2 Table of contents

• 1 Lectures
  • 1.1 Bioinformatics Basics
  • 1.2 Comparing Gene Sequences
  • 1.3 Comparing Gene Sequences 2
  • 1.4 Gene Finding
  • 1.5 Locating genes and its functions: techniques, problems and difficulties
• 2 Practical Lessons
  • 2.1 Basic R and generic data
    • 2.1.1 Basic R
    • 2.1.2 Files
    • 2.1.3 Gene Sequences
    • 2.1.4 Comparing Gene Sequences
    • 2.1.5 Control: Loading and processing data
    • 2.1.6 Programming Exercises
  • 2.2 Basic analysis of genetic data
    • 2.2.1 GC Content
    • 2.2.2 Subseries GC Content
    • 2.2.3 Exercise: Comparing sequences
    • 2.2.4 Creating dot plots
    • 2.2.5 Loading and comparing data
  • 2.3 Codons and gene finding
    • 2.3.1 Translating bases to codons
    • 2.3.2 Codon frequencies and finding genes
    • 2.3.3 Theoretical Control
    • 2.3.4 Aminoacid sequences and base sequences
  • 2.4 Summary and exam
    • 2.4.1 Theoretical Questions
    • 2.4.2 Final exam