Structure Content

CapsuleFinder is a program that detects capsule systems with high accuracy in proteic sequences.  It is based on the use of HMM profiles for the detection of the essential proteins of capsule biogenesis and  requires computational models describing […]

checkMyIndex is an application whose goal is to help in finding a set of compatible indexes for a sequencing experiment. It has been developped using the R/Shiny environment and is freely available at https://checkmyindex.pasteur.fr/. […]

A new adapter removal program for next generation sequencing Clean-ngs is available on GitHub: https://github.com/PF2-pasteur-fr/clean_ngs For more information contact Bernd Jagla  

Warning: This data is old and the site will be discontinued soon. We are working on an alternative. This website allows to query a dataset of 947 conjugative systems, 646 non-conjugative T4SS and 1,180 […]

The genomic and nomenclature databases of strains of pathogenic bacterial species are available through the Institut Pasteur BIGSdb portal: http://bigsdb.pasteur.fr. The portal is powered by the Bacterial Isolates Genome Sequence DataBase (BIGSdb) tool developed […]

Warning: This data is old and the site will be discontinued soon. We are working on an alternative. Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial […]

sequana_coverage is a standalone application that reports genomic regions of interest (ROIs) which are significantly over- or under-represented in high throughput sequencing data. Thanks to HTML reports, is allows users to browse the detected […]

The single cell transcriptomics, epigenetic and genomics are supported by collaborative effort of the CB UTechS, Biomics and the Hub. The CB UTechS gathers expertise and high-end instrumentation for single cell phenotyping and sorting, single cell […]

Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane: Shigella, Escherichia coli, Yersinia pestis, Salmonella, Pseudomonas aeruginosa, Helicobacter pylori, Vibrio cholerae, etc. Protein secretion systems are […]

The database TXSSdb includes all results from our works on the detection of protein secretion systems in 1,528 complete genomes of bacteria with diderm-LPS cellular enveloppes. It is by far the most complete database […]