Eduardo Rocha

Bacteria face many unexpected challenges, which require responses that may be difficult to prepare. This is often the case of antagonistic biotic interactions, e.g. when phages infect bacteria, which are regulated by evolutionary processes […]

Towards the design of new nitrogen fixing symbionts Elucidate how the capacity to establish a nitrogen fixing symbiosis with legumes has been acquired by new bacterial taxons via a lab-evolution experiment should allow developping […]

Bacterial genomes are mainly composed of two types of replicons: chromosomes and plasmids. Plasmids are accessory mobile genetic elements acquired by horizontal transfer between strains or species. Their domestication by new hosts is of […]

Prokaryotes evolve rapidly new functionalities by horizontal gene transfer delivered by mobile genetic elements (MGE). MGE increase relatedness between individuals and thereby might also promote the establishment of microbial social networks. Many studies have […]

Replication-associated gene dosage effects Maximal growth rates are central to microbial life-history strategies because there is a trade-off between fast growth in copiotrophs and scavenging potential in slow-growing oligotrophs. When E. coli’s generation time […]

The evolutionary roles of repeats Stress is often faced in nature, whether from lack of nutrients, arrival of competitors or predators, or the presence of toxic substances. The survival of stressed organisms can be […]

Bacteriophage–bacteria interactions are affected by phage satellites, elements that exploit phages for transfer between bacteria. Satellites can encode defense systems, antibiotic resistance genes, and virulence factors, but their number and diversity are unknown. We […]

The CRISPRCasFinder program enables the easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program […]

The study of the gene repertoires of microbial species, their pangenomes, has become a key part of microbial evolution and functional genomics. Yet, the increasing number of genomes available complicates the establishment of the […]

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 […]

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 […]

While there were efficient methods for detecting strict repeats or detecting already characterised repeats, there was no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in […]

Intragenic duplications of genetic material have important biological roles because of their consequences in terms of protein sequence and structure. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically […]

Growthpred predicts bacterial minimal doubling times by analysing codon usage bias in genomes and metagenomes. The program takes a set of DNA protein coding sequences, searches for ribosomal protein coding genes and translates all […]

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 […]

Repeatoire is a bioinformatics tool for locating DNA repeats inside of sequenced (but not necessarily assembled) genomes. Specifically, our focus is on repeat families, i.e. related sets of repeats that share a similar role […]

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 […]

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 […]

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 […]

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 […]