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This Week in Nucleic Acids Research: Nov 14, 2012

In the early, online version of Nucleic Acids Research, the National Institute of Allergy and Infectious Diseases' Alison McBride and her colleagues report on a repository for papillomavirus genomic sequence-related data. The web-based resource, dubbed Papillomavirus Episteme, or PaVE, is freely available to members of the research community, study authors say, and is home to data on hundreds of papillomavirus genome sequences. The site also contains sequence information for thousands of papillomavirus genes and proteins, along with structural data for a few dozen of its viral proteins.

Meanwhile, a team from North Carolina State University and the Mount Desert Island Biological Laboratory describes a database called the Comparative Toxicogenomics Database that focuses on interactions between genetics and response to various chemical exposures. That site currently contains information on more than 15 million such relationships, the team reports, ranging from chemical-gene or chemical-disease interactions to interactions between genes and disease. "This wealth of chemical-gene-disease data, combined with novel ways to analyze and view content, continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases," say first author Allan Peter Davis, of North Carolina State University, and his co-authors.

Among the other databases included in a collection of Nucleic Acids Research studies currently available online is a spliceosome database that can be used for exploring the various sets of small nuclear RNAs and proteins that come together to contribute to pre-messenger RNA splicing. As University of California at Santa Cruz's Melissa Jurica and co-authors write, the site compiles information on spliceosome-related gene names, orthologs, identifiers, and more, as well as tools for tracking the spliceosome assembly stages. Together, they say, these data "provide an easy reference for spliceosome components and will support future modeling of spliceosome structure and dynamics."

The Scan

Nucleotide Base Detected on Near-Earth Asteroid

Among other intriguing compounds, researchers find the nucleotide uracil, a component of RNA sequences, in samples collected from the near-Earth asteroid Ryugu, as they report in Nature Communications.

Clinical Trial Participants, Investigators Point to Importance of Clinical Trial Results Reporting in Canadian Study

Public reporting on clinical trial results is crucial, according to qualitative interviews with clinical trial participants, investigators, and organizers from three provinces appearing in BMJ Open.

Old Order Amish Analysis Highlights Autozygosity, Potential Ties to Blood Measures

Researchers in BMC Genomics see larger and more frequent runs-of-homozygosity in Old Order Amish participants, though only regional autozygosity coincided with two blood-based measures.

Suicidal Ideation-Linked Loci Identified Using Million Veteran Program Data

Researchers in PLOS Genetics identify risk variants within and across ancestry groups with a genome-wide association study involving veterans with or without a history of suicidal ideation.