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 TekaiaInstitut Pasteur

tekaia@pasteur.fr

Why this course ?

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

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

2 5 12 19 24 42 71 116 165 224323

471700

916

2203

3847

4424

115

0200400600800

10001200140016001800200022002400260028003000320034003600380040004200440046004800

95 96 97 98 99 00 01 02 03 04 05 06 07 08 09 10 11 12Year

Number Complete Genome Sequencing Projects

05-2012

13679 Projects

Mathematics Statistics

Nucleotide & protein sequences and related

informations

InformaticsBiology

Bioinformatics

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

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;

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.

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Evening lecture at 8:00 Mme Christiane Groben:

Freedom for Research: Anton Dohrn and Science management

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Thanks

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