Comparative Genomics Applied to Prokaryotic Analysis
9:0010:00
Monday , August 10th
DATA SOURCES IN
GENOMICS
Biological concepts:
 Next Generation
Sequencing
 Genetic Variation (Genomic
Plasticity)
 TB Evolutionary history
Tuesday, August 11th
CORE-GENOME, PANGENOME, SYNTENY
Biological concepts:
 Genome structure
 Synteny
 Gene structure
 Gene homology
 Core-genome/Pangenome
10:0011:00
Computational concepts:
 Sequence alignment
 NGS mapping and assembly
 Overview of phylogeny
inference algorithms
 NCBI databases
Wednesday, August 12th Thursday, August
13th
Andreas Tauch
Plenary talk: A
decade of
Corynebacterium
jeikeium research:
From genomics to the
design of new
deodorants
Computational concepts: continued
 Overview of suffix trees
applications
 Homology identification
 Overview of algorithms
for gene prediction in
prokaryotes
 Overview of overlap
layout consensus graphs
11:0012:00
Practical analysis:
 Computational
environment
 Query, download and
data organization
Practical analysis:
Gene sequence alignment
core-genome exercise
Arwa Al-Dilaimi
Talk: Corynebacterium
vitaeruminis and its
potential for vitamin
production – an
example for
comparative
corynebacterial
genomic
Arwa Al-Dilaimi
Talk: Genome and
transcriptome of the
new species
Corynebacterium
glyciniphilum – an
example for
corynebacterial
transcriptomics
Arwa Al-Dilaimi
Associated software
demonstration:
Application of
ReadXplorer for
detecting the
transcriptional
landscape of
microbes
Friday, August 14th
GENOMIC STRUCTURAL
VARIANTS
Practical analysis:
 Transposons and Insertion
Sequences
 Phages
 CRISPR-Cas and VNTR locus
 Pathogenicity island
identification
 Synteny blocks contiguity
analysis
 Visualization with Circos
Results interpretation:
 Genome annotation
visualization
Andreas Tauch
Strategy talk: The
German Network for
Bioinformatics
Infrastructure
APPLICATIONS
GENOMIC
STRUCTURAL
VARIANTS
Biological concepts:
Computational concepts:
Biological concepts:
 Genotyping
 Variants associated with
antibiotic resistance
12:0014:00
Lunch
14:0016:30
Practical analysis:
Practical analysis:



 Gene sequence alignment
Variant identification
TB lineage identification
Phylogeny inference
pan-genome exercise
 Homology exercise
 Harvest Suite core-genome
exercise
 Sibelia synteny blocks
exercise
Arwa Al-Dilaimi
Associated software
demonstration:
Application of GenDB
for microbial genome
annotation
Arwa Al-Dilaimi
Associated software
demonstration:
Application of EDGAR
for comparative
microbial genome
analysis





Results interpretation:


Genome collection
Variome statistics and
figure
Results interpretation:
 Comparison of core-
genomes using Venn
diagram
 Pan-genome curve
 Synteny visualization
 Homology report
Arwa Al-Dilaimi
Short Talk: My
experience with Vibrio
cholerae isolated from
a Brazilian university
campus
Phages
CRISPR-Cas and VNTR
locus
Pathogenicity islands


Selecting SNPs for
discrimination

Classifier performance
evaluation
Practical analysis:

SNPs for lineage
discrimination

Primer design for antibiotic
resistance identification
TB lineages
Computational
concepts:

16:3017:00
Transposons and
Insertion Sequences

Sequence alignment
applications for
identification of large
variations
Contiguity analysis
Structural variants
representation
Results interpretation:

Simulated performance
measures
 Conclusions and
perspectives