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This Week in Nucleic Acids Research: Apr 10, 2019

A team from Sweden, Australia, and Canada introduce an algorithm — called "analysis of translational activity," or anato2seq — for gauging messenger RNA translation shifts. Using continuous DNA array-based polysome profiles or RNA sequence-based mRNA counts, the approach can "identify and separate changes in translational efficiency affecting protein levels and translational buffering," the authors say, noting that "in contrast to available analytical methods, anota2seq also allows specific identification of an underappreciated mode of gene expression regulation whereby translation acts as a buffering mechanism which maintain protein levels despite fluctuations in corresponding mRNA abundance ('translational buffering')." The investigators applied anota2seq to simulated RNA-seq data, demonstrating that it could statistically tease out translation changes related to both translational buffering and protein levels. 

Researchers in Canada and Australia describe a freely available, functionally annotated bacterial tree of life, known as AnnoTree. The current iteration of AnnoTree encompasses interactive data for more than 27,000 bacterial genomes and genome sequences for 1,500 archaea profiled with taxonomic, phylogenetic, and functional annotation, the team explains. When investigators tapped into this data to look at the distribution of more than 28,300 gene or protein families in the context of prokaryotic phylogeny, for example, they saw "phylogenetic patchiness" for families of genes related to antibiotic resistance and other processes. "We anticipate that AnnoTree will be a valuable resource for exploring prokaryotic gene histories," they write, "and will act as a catalyst for biological and evolutionary hypothesis generation."

A pair of investigators from Biobyte Solutions and the European Molecular Biology Laboratory outlines updates present in the latest version of a free, online tool for visualizing, annotating, and analyzing phylogenetic trees. The "interactive tree of life" (iTOL) v4 includes several updates related to annotation, dataset editing, data display, user accounts, and other features, the researchers report, noting that iTOL v4 makes it possible to visualize phylogenetic trees developed with the Quiime 2 software package. The tool can tackle more than 700,000 trees generated by tens of thousands of users, they report.