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Description
The course will be held at KMUTT (King Mongkut's University of Technology Thonburi) in Bangkok, Thailand. This is the third workshop on Comparative Microbial Genomics held in Thailand. (The previous two workshops were held in 2005 and in 2008). The workshop will focus on methods to compare bacterial genomes, and is a one-week version of the DTU course 27104 taught in Denmark. The general format is lectures in the morning, and computer exercises in the afternoon. The workshop will be presented by Dave Ussery, leader for the Comparative Microbial Genomics group [link to publications], and the computer exercises will be assisted by Karin Lagesin (in Oslo, Norway).
Pictures
Link to pictures from the workshop.
Course outline
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Monday, 8 March |
Tuesday, 9 March |
Wednesday, 10 March |
Thursday, 11 March |
Friday, 12 March |
9:30-10:30
| Introduction to Genomics
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Methods to Compare Genomes
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Expression of Genes and Proteins
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Pan- and core-genomes
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Summary
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10:30-11:00
(Coffee Break)
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11:00-12:00
Sequences as biological information
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Genome Annotation
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Comparison of Bacterial Proteomes
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Microbial Communities
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Group presentations
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12:00-13:00
(Lunch break)
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13:00-15:00
Downloading Genomes |
finding RNA genes
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BLAST matrices
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Pan- Core-genome plots
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Group presentations
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15:00-15:30
(Coffee break)
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15:30-17:00
Prediction of genes |
Construction of 16S rRNA trees
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Genome atlases
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BLAST atlases
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Group presentations, certificate presentation, closing
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Monday, 8 March, 2010: DNA and Genomics [chapters 1-5 of text]
Tuesday, 9 March, 2010: RNA and Transcriptomics [chapters 6-9 of text]
| 9:30-10:30 | Lecture: Methods to Compare Genomes
Links: PDF Slides "Ten Years of Sequencing Bacterial Genomes",Functional and Integrative Genomics 6:165-185, (2006). |
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| 10:30-11:00 | Coffee break |
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| 11:00-12:00 | Lecture: Genome Annotation
Links: PDF Slides "On the Total Number of Genes and Their Length Distribution in Complete Microbial Genomes", Trends in Genetics, 17, 425-428, (2001).
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| 12:00-13:00 | Lunch break |
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| 13:00-17:00 | Exercise- Build your own Genomic Databases - Part 2: Finding RNA Genes and building a 16S rRNA tree
Links: "RNAmmer: consistent and rapid annotation of ribosomal RNA genes", Nucleic Acids Research, 35, 3100-3108, (2007). |
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Wednesday, 10 March, 2010: Proteins and Proteomics [chapters 10-11 of text]
Thursday, 11 March, 2010: Microbial Communities [chapters 12-14 of text]
Friday, 12 March, 2010: Student Presentations
Link to pdf of talk
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This file was last modified Thursday 11th of March 2010 13:04:49 GMT |
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