A German-led team describes a reference database system called BACTOME for analyzing everything from phylogeny and evolution to genetic diversity and adaptation in clinical isolates of Pseudomonas aeruginosa with DNA sequence, RNA sequence, and pathogen phenotype information. The database makes it possible to assess P. aeruginosa based on specific gene, isolate, or phenotype features, the researchers say. They note that BACTOME also "provides a compilation of DNA sequences and gene expression values of a plethora of clinical isolates to give a consensus DNA sequence and consensus gene expression signature."
Researchers from Cornell University, the US Department of Agriculture's Agricultural Research Service, and elsewhere share potential applications for the Cucurbit Genomics Database (CuGenDB), a database for storing, integrating, visualizing, and analyzing genomic and transcriptomic data for pumpkin, melon, cucumber, and other plants in the Cucurbitaceae family. Along with cucurbit genome sequences, genetic maps, transcriptomic data, and more, the team reports, the CuGenDB contains annotation information and tools for doing comparative and functional analyses. Among them: new tools for taking a look at genome synteny and gene expression features.
Finally, a team from Spain presents PopHumanScan, an online catalog that aims to spell out parts of the genome that have been subject to selection in human populations, based on a new analysis of data from the 1000 Genomes Project. For this initial analysis, the researchers used their PopHumanScan pipeline to assess eight population genetic statistics to sequences from 22 non-admixed populations, uncovering selective sweeps and recurrent positive selection events. "Designed as a collaborative database, PopHumanScan aims to become a central repository to share information, guide future studies, and help advance our understanding of how selection has modeled our genomes as a response to changes in the environment or lifestyle of human populations," the authors write.