Bioinformatics: An introduction

This simulation replaces the previous “Plant Transcriptomics” simulation.

What if you could engineer a metabolic pathway from a rare plant into another organism and produce an antimalarial compound at large scale? In this simulation, you will learn how to identify the genes that encode specific enzymes. You will use a method called RNA-seq to quantify the transcription of different genes. Use this information to narrow down the candidate genes by using bioinformatics tools.

Find a novel antimalarial compound

Your mission starts with analyzing a plant sample from the Amazon rainforest. A group of local tribal people use this rare plant to cure malaria. A phytochemist identifies the antimalarial compound. Your task is to identify the enzymes responsible for the production of this potential drug.

Learn how molecular compounds are produced and extract the RNA

Your next task will be to identify an enzymatic pathway that converts the precursor molecule into the antimalarial component. If you want to produce this compound at large quantities, you will need to transform the enzymatic pathway into another organism. To do so, you must identify the genes encoding the enzymes. All the information you need is contained within the composition of mRNA molecules in different plant tissues.

Learn about the structural difference of mRNA and DNA and perform RNA-seq

The key to the functions of mRNA and DNA is their structures. While the lab assistant is reverse transcribing your mRNA sample into cDNA, you will be learning about the structure of these two amazing molecules. Your next task is then to perform Next Generation Sequencing (NGS) of your cDNA sample. You will sequence the cDNA of different plant tissues to determine the sequence and expression of the target enzymes. An animation will show you what is going on inside the flow cell enabling you to see how millions of different sequences can be read in parallel.

Analyze your results using phylogenetic analysis and BLAST

Like a true detective, you will analyze the huge amount of NGS reads and determine which enzyme is most likely involved in the biosynthesis of the antimalarial compound. You will learn how relatedness of DNA sequences can be used to identify unknown enzymes and learn the basics of sequence comparisons.

Will you be able to identify the enzymes and produce a novel drug that can save millions of people?