Computational Biology


If you are an accomplished coder, then you can write a separate program for every new task you encounter. In practice, these programs only need to be written once and packaged into modules, where those of us who are not great coders can use them quickly and efficiently. In this first series of exercises, we will familiarize ourselves with a sampling of some of the more popular bioinformatics tools taken from “out of the box” software. In preparation:

  • read chapter 00 in the textbook: Prologue
  • get yourself familiar with the BioPython module
Title Class progress
Counting DNA nucleotides
Transcribing DNA into RNA
Translating RNA into protein
Introduction to protein databases
Finding genes with ORFs
Protein translation
Complementing a strand of DNA
Computing GC-content
Finding a motif in DNA
Consensus and profile
Locating restriction sites
RNA splicing
Enumerating k-mers lexicographically
k-Mer composition