Skip to main content
Premium Trial:

Request an Annual Quote

Nucleic Acids Research Papers on PaintOmics 4, PADLOC Web Server, CircadiOmics

An international team led by investigators at Cardiff University, the Spanish National Research Council, and the University of Florida outlines a tool known as PaintOmics 4 that brings in biological pathway clues for analyzing multi-omics datasets. The team notes that the current version of the integrative analysis and visualization tool is compatible with KEGG, REactome, and MapMan pathway databases, while allowing for metabolite, regulatory, and other analyses. "We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology," the authors write, noting that the latest version of the tool "addresses some of these current limitations in pathway definitions, metabolomics data integration, and visualization across molecular layers."

Investigators at the University of Otago and centers in the UK and Spain present a web server designed to accompany "Prokaryotic Antiviral Defense Locator" (PADLOC) — a bioinformatics method for detecting microbial genome features involved in antiviral defense. Along with capabilities for finding a wide range of CRISPR arrays and other antiviral defense systems from metagenome, genome, contig, or other bacterial, phage, or archaeal sequences, the team notes, the web server currently contains defense system data gleaned from more than 230,000 RefSeq genomes. "PADLOC will continue to evolve as new defense systems are discovered and additional biological insight allows us to fine-tune the parameters of identification," the authors write, adding that "comprehensive identification of many systems made possible with PADLOC also opens avenues for investigating many interesting biological questions."

Finally, a research team at the University of California, Irvine and the University of South Carolina describes an analytic web server, annotated repository, and visualization tool focused on transcriptomic, metabolomic, proteomic, and other omics-based circadian rhythm research. The "CircadiOmics" web portal encompasses data spanning more than 100 million measurements made through hundreds of experiments spanning dozens of species, organ, and tissue types. "The large repository of omic data available via CircadiOmics serves as an invaluable resource to analyze the complexity of circadian mechanisms and their downstream implications," the authors suggest, arguing that the "CircadiOmics interface is especially advantageous and unique because it allows users to easily perform comparative analyses and aggregated inferences about circadian rhythms at the molecular level across species, tissue/organs, and genetic, epigenetic, and environmental conditions."