Research / Core Facilities / Genopole / Bio-informatics & Bio-statistics

Bio-informatics, bio-Statistics and databases

The platform provides genotyping data analysis software, can contribute to the development of bioinformatics and statistic tools and maintains and curates databases that allow the international coordination on the nomenclature of bacterial genotypes as well as of beta-lactamase enzymes responsible for the resistance to antibiotics.

Expertise in data analysis

The platform proposes :
  • A support in biostatistics : design of experiments, data processing and analysis, hypothesis testing.
  • A support in bioinformatics : design of oligonucleotides, use of software...
  • Bioinformatics tools can be developed at the platform according to the requirements of the different collaborative projects. For more important developments, a collabortion with informatics/bioinformatics group is possible.
  • A scientific expertise in the domain of population genetics, phylogeny and evolution of infectious agents

Analysis tools

The platform provides access to the following software :

BioNumerics v6.6 (Applied Maths, Belgium www.applied-maths.com/) which allows the storage and analysis of different types of data (sequences, banding profiles, biochemical data...) for the genetic characterization of pathogens in the context of surveillance and microevolution.

GeneMapper®v4.0 (Applied Biosystems USA,www.applied-biosystems.com) which allows the sizing of DNA fragments separated by capillary electrophoresis.
It is used to analyze micro-or minisatellites for genotyping or population genetics studies in bacteria, fungi and insect vectors.

MLST databases
Multilocus Sequence typing (MLST) is a reference approach to determine the genetic structure of bacterial populations and the international epidemiological follow-up of emerging clones.

Our platform provides access and curates MLST databases for numerous species of pathogens such as Klebsiella pneumoniae, Listeria monocytogens and
Acinetobacter baumannii.
Access to databases at www.pasteur;fr/mlst

MLVA-NET: a standard system for MLVA-VNTR typing

MLVA-NET is a flexible and open system meant to host and analyze MLVA-VNTR (minisatellite/microsatellite) data for haploid microorganisms.
Inspired by the MLST databases concept, this system was developed by the platform and allows the international standardization of MLVA genotype designations.
Access to MLVA-NET
                                       
 

CRISP database

The CRISP markers (Clustered Regularly Interspaced Short Palindromic Repeats) found in numerous bacterial genomes allow the typing of strains in certain bacterial species such as Salmonella and Legionella.

Access to http//:www;pasteur.fr/recherche/genopole/PF8/crispr/CRISPRDB.html

LEN, OKP,and OXY beta-lactamase variants

The beta-lactamases significantly contribute to bacterial resistance to beta-lactam antibiotics (penicillins, cephalosporins...). The specific characterization of these enzymes is useful to optimize the patient's treatment and for epidemiological follow-up of resistance.

Our platform is in charge of the international stnadardization of the nomenclature of LEN, OKP and OXY enzymes.

Access to www.pasteur.fr/ip/easysite/pasteur/en/research/plates-formes-technologiques/pasteur-genopole-ile-de-france/genotyping-of-pathogens-and-public-health-pf8/beta-lactamase-enzyme-variants/beta-lactamase-enzyme-variants