Expertise group : ALPS – Algorithmics and programming in science

We obtained recent evidence that CD4+ T cells of HIV Controllers preferentially express a particular set of shared T cell receptors (TCRs) directed to the HIV capsid. We will  monitor the dynamics of these […]

The protozoan parasite Leishmania donovani causes fatal visceral leishmaniasis, one of the most neglected tropical diseases. In the absence of economic incentive, serious Research and Development (R&D) investments into anti-leishmanial drug development lack from […]

Bioweb is a web portal to search and access the bioinformatics resources available at the Institut Pasteur. It provides an overview of the resources available in the central infrastructure, as well as features to identify […]

For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to […]

Rapid Peptides Generator (RPG), is a standalone software dedicated to predict proteases-induced cleavage sites on sequences. RPG is a python tool taking a (multi-)fasta/fastq file of proteins as input and digest each of them. […]

CRAW is a package which aim to compute and visualize the coverage of RNA seq experiments. The main feature of this tools is the coverage is computed on the both strands, and is centred […]

JASS is a python package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface. The generation of joint […]

SynTView is a comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic […]

SHAMAN is a SHiny Application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. SHAMAN is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, […]

This program demultiplexes fastq data having “in-line” barcodes, based on a given list of barcodes and a barcode start position. It tries to assign each fastq record to the most likely barcode, taking into […]

Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include […]

IntegronFinder is a program that detects integrons in DNA sequences. The program is available on a webserver (Galaxy), or by command line (IntegronFinder on github). It is now in its second version. Integrons are […]

BPM is a software for exact pattern matching of DNA. It can be seen as a DNA multi “grep”. First, the tool preprocess a bunch of DNA patterns to create an index. Then, the […]

Listeriomics integrates all complete genomes, transcriptomes and proteomes published for Listeria species to date. It allows navigating among all these datasets with enriched metadata in a user-friendly format. listeriomics.pasteur.fr The main purpose of the website is […]

Scans a set of protein sequences for type IV secretion systems and relaxases using HMM profiles. See Guglielmini et al. (2011) for our criteria to class loci on the basis of this output. Except […]

COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. Directly from non-assembled reads, all against all comparisons are performed through an efficient indexing strategy. Then, results […]

Compareads is a tool designed to extract similar reads between potentially huge metagenomic datasets (i.e., hundreds of millions reads per dataset)

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 […]

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 […]

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 […]