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CBS >> CBS Courses >> Comparative Microbial Genomics Workshop >> Course Programme

Description

The course will be held in Auditorium LS41 Laboratoriesenteret, St. Olaf's Hospital, NTNU, Trondheim, Norway. The workshop will focus on methods to compare bacterial genomes, and is a short 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 Thomas Dybdal Pedersen.




Course outline

  Monday, 14 May Tuesday, 15 May Wednesday, 16 May
9:30-10:30
Introduction to DNA Atlases
BLAST Matrices
Group presentations
10:30-10:45
(short Break)
 
10:45-11:30
3 Generations of Genome Sequencing
Bacterial core- and pan-genomes
Group presentations
11:30-13:00
(Coffee Break)
 
13:00-16:30
Computer exercises:
GenomeAtlas construction, Amino acid and Codon Usage
Computer exercises:
Construction of 16S rRNA trees, Pan- core-genome plots
Group presentations


Book Cover The textbook is written specifically for this course:
COMPUTING FOR COMPARATIVE GENOMICS: Bioinformatics for Microbiologists
by David W. Ussery, Stefano Borini, and Trudy M. Wassenaar

Springer, published in spring, 2009.       Link to Amazon.com



Monday, 14 May, 2012: DNA, RNA and Genomics

9:30-10:30Lecture: Introduction to DNA Atlases     PDF of Talk
10:30-11:00Coffee break
11:00-12:00Lecture: 3 Generations of Sequencing Technology     PDF of Talk
12:00-13:00Lunch break
13:00-17:00Computer Exercises


Literature: Chapters 1-6 of textbook
Link to PDF of "RNAmmer" paper (PMID 17452365)
"Comparison of 61 Sequenced E. coli Genomes", Microbial Ecology, 60:708-720, (2010).
"Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream", Nature Biotechnology, 27:627-632, (2009).





Tuesday, 15 May, 2012: Proteins and Proteomics


9:30-10:30Lecture: BLAST Matrices, Atlases     PDF of Talk  
10:30-11:00Coffee break
11:00-12:00Lecture: Bacterial pan- and core-genomes     PDF of Talk  
12:00-13:00Lunch break
13:00-17:00Computer Exercises - Part 2: Prediction of Protein-encoding Genes; Construction of a BLAST Matrix, and a BLAST Atlas


Literature: Chapters 7-9 of textbook
Link to PDF of "BLAST Atlas" paper (PMID 18414733)
Link to PDF of "BLAST Matrix" paper (PMID 15632419)





Wednesday, 14 December, 2011: Conserved genes within a group of bacteria: Vibrio cholera as an example.


9:30-10:30Lecture: Vibrio genomics     PDF of Talk
10:30-11:00Coffee break
11:00-12:00Student Presentations
12:00-13:00Lunch break
13:00-17:00Presentations


Literature: Chapters 10-14 of textbook
Link to "Standard operating procedure for computing pangenome trees" paper (PMID 21304685)
Link to "Microbial comparative pan-genomics using binomial mixture models." paper (PMID 19691844)
Link to "The Salmonella enterica Pan-genome." paper (PMID 21643699)










This file was last modified Thursday 28 June, 20112 15:25:26