Introduction to Bioinformatics

This course has two goals. The first one is to introduce students to bioinformatics, the data it uses and its methods. The second one is to teach students basic programming in R, and to use bioinformatics libraries. At the end of this course, the student should be able to find gene sequences in the internet, and to do simple analysis with them.

Besides the usual grading at each lesson, there will be a periodic practical control after each block of four lectures. It will consist of a test done in the computer where the student will have to execute a task with a visible result using R programming and data sets.

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