Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria.

Background: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens.

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies.

Motivation: Genome sequencing projects sometimes uncover more organisms than expected, especially for complex and/or non-model organisms. It is therefore useful to develop software to identify mix of organisms from genome sequence assemblies.

Results: Here we present PhylOligo, a new package including tools to explore, identify and extract organism-specific sequences in a genome assembly using the analysis of their DNA compositional characteristics.

Listeriomics: an Interactive Web Platform for Systems Biology of .

As for many model organisms, the amount of omics data produced has recently increased exponentially. There are now >80 published complete genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians.