1. Bioinformatics and Comparative Genome Analyses Course Course web page: http://www.pasteur.fr/~tekaia/BCGA2012.html EMBO Bioinformatics and Comparative Genome Analyses Course Stazione Zoologica Anton Dohrn, Naples, Italy, May 7 - 19, 2012 EMBO Bioinformatics and Comparative Genome Analyses Course Stazione Zoologica Anton Dohrn, Naples, Italy, May 7 - 19, 2012 Introduction Fredj Tekaia Institut Pasteur tekaia@pasteur.fr

2. Why this course ?

3. 2847 153 173 GOLD: http://www.genomesonline.org/ Tree of life 13679 total projects: Complete genomes 3173 projects 2079 published 1094 Permanent Drafts (2012/05/02) Ongoing: 7908 Bacteria 213 Archaea 2385 eukaryotes Metagenomes: 334

4. Evolution of the number of complete genome sequencing projects Complete sequencing genomes span the three domains of life http://www.genomesonline.org/cgi-bin/GOLD/bin/gold.cgi 05-2012 13679 Projects

5. MathematicsStatistics Nucleotide & protein sequences and related informations Informatics Biology Bioinformatics

6. The main objectives of the course are to familiarize participants with bioinformatics and large scale genome data analyses skills by introducing: 1- advanced fundamental algorithms used in Bioinformatics; 2- their application in genome analyses; 3- recent knowledge acquired from genomes studies and their perspectives. Bioinformatics and Comparative Genome Analysis

7. Main Lecture/practical topics include: Genomes comparisons: Technical aspects - writing scripts; - Methods applied to families of genes/proteins: multiple alignments, phylogeny analyses; -Determination of paralogs - orthologs and clustering; - Genome visualization (Circos); - Genomes alignments; Next Generation Sequencing: Methods and Tools; Chip-Seq: Methods and applications; Microarray: Methods for gene expression analyses; Protein-Protein Interactions;

8. Lectures on specific topics and perspectives: Base composition variability in vertebrate genomes; Realistic Models and Efficient Algorithms in Bioinformatics/Biophysics Analyses of Genomes; Transcriptome mining: examples of meta-analysis using gene expression data; Eukaryotic Genomes and Evolution.

9. Evening lecture at 8:00 Mme Christiane Groben: Freedom for Research: Anton Dohrn and Science management

11. Thanks