Course Information
- This is the bioinformatic tutorial for week 11 of the course 27255 - Advanced Experimental Prokaryotic Molecular Biology and Ecology (Spring 2023) held at DTU Bioengineering.
- Introduction to lab-work: Building 202/Room 7001
- Lab work: Building 202/Room 7007
Introduction and Overview
- On the last part of the course (week 10-12), you will learn how to obtain and analyze the DNA sequence of selected isolates to mine the DNA for relevant genetic information. First, you will extract DNA from your isolated pseudomonas (two per group) and subsequently prepare the DNA of a selected isolate for sequencing (one per group). The actual sequencing will be done using Nanopore MinION, a 3rd generation sequencing platform capable of real-time sequencing of very long reads (>200kb). You will perform sequence-based analysis using several online tools that will be presented in this tutorial.
- In your analysis, you will specifically focus on: potential secondary metabolites, metabolic capabilities, antimicrobial resistance and pathogenicity. The overall aim of week 10-12 is to obtain genomic information and study how it correlates with the phenotypic data you have obtained in the previous weeks. Finally, you will use all the data you have obtained throughout the course to evaluate your isolated strains’ potential and suitability as a production strain or for commercial use.
| Week | Task and Goals | ||
|---|---|---|---|
| Week 10 | Genomic DNA preparation Minion | Genome sequencing using Minion (Oxford Nanopore Tech) | Initiate data analysis pipeline construction |
| Week 11 | Pipeline construction and analysis | Gene annotation and analysis | |
| Week 12 | Genome analysis | Correlations between genomic and phenotypic data | Poster preparation |
Prerequisites
Before starting the bioinformatics analysis, make yourself comfortable with the Galaxy platform by following the tutorials from the Galaxy Training Network. I would recommend trying these two tutorials: