Evolutionary Microbial Genomics

Unit head: Eduardo P C Rocha


Scientific activities of the Evolutionary Microbial Genomics Unit are centered on the bioinformatics and biostatistics analysis of genomes, at the crossroads of molecular evolution, population genetics, evolutionary ecology and molecular genetics.


We focus on four major questions: 1) How and why are genomes organized? 2) How are such organizational features evolving in face of the extensive genome dynamics? 3) What are the roles of mobile elements in the trade-offs between organization and dynamics? 4) What is the interplay between genome dynamics and bacterial pathogen emergence at the microevolutionary and epidemiological scale?



Génomique évolutive des microbes
Institut Pasteur
Centre François Jacob
28 rue du Dr Roux
75724 Paris cedex 15

Tel: 0033 (0)1 40 61 33 53
Fax: 0033 (0)1 45 68 87 27
mail: erochaATpasteur.fr



  • Swelfe, identification of degenerate repeats in genes, proteins and 3D structures.
  • Repseek, identification of degenerate repeats in genomes.
  • Repeatoire, ab inito prediction of repeat families.
  • GrowthPred, prediction of growth-related traits in microbes from genomic and metagenomic data.
  • T3SSscan- FLAGscan, prediction of protein secretion systems in diderms (prokaryotes).
  • CONJscan-T4SSscan, search for relaxases and key components of type IV secretion systems in proteomes using an HMM profiles database.
  • MacSyFinder provides a flexible framework to model and identify molecular systems.


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