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Description

This workshop on comparative microbial genomics will focus on methods to compare hundreds of bacterial genomes. The general format is lectures in the morning, and computer exercises in the afternoon. We will be using the textbook COMPUTING FOR COMPARATIVE GENOMICS: Bioinformatics for Microbiologists, by David W. Ussery, Stefano Borini, and Trudy M. Wassenaar. You can download a pdf of the textbook but note that this is a fairly large file (88 Mb), and might take awhile, depending on the speed of our connection. Note that this link will only work for the duration of the course!

Course outline

Monday, June 2 Tuesday, June 3 Wednesday, June 4 Thursday, June 5 Friday, June 6  
1 
Introduction to Genomics
David Ussery
5 
Methods to Compare Genomes
David Ussery
9 
Regulation of Gene Expression
David Ussery
13 
Pan-, core- and metagenomes
David Ussery
17 
An overview and questions for students
David Ussery
9:00-10:30
 
10:30-10:45
Break
2 
Introduction to Web Services
Peter Hallin
6 
Non-coding RNA genes
David Ussery
10 
Proteins, Genomes, and Proteomes
David Ussery
14 
Evolution and the origins of bacterial species
David Ussery
18 
BLAST atlases, core/pan genome plots
Peter Hallin
10:45-12:00
 
12:00-13:00
(Lunch break)
3 
Annotation part I:
Gene finding
Peter Hallin
7 
Annotation, part 2: RNA genes
Peter Hallin
11 
Prediction of promoters
Peter Hallin
15 
Methods for proteome comparison
Peter Hallin
19 
Networking
13:00-13:30
4 
Fetching genomes and predicting protein coding
genes
Peter Hallin
8 
rRNA and tRNA predictions
Peter Hallin
12 
Codon usage, promoters, BLAST atlases
Peter Hallin
16 
16S trees, BLAST matrices, 2-D clustering of results
Peter Hallin
20 
Networking, certificate presentation, closing
13:30-17:00