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Metagenomics-RAST server, Sequin 9.00, Cosmic 40

Researchers from Argonne National Laboratory, the University of Chicago, and San Diego State University have developed a metagenomics-RAST server, a public resource for the automated analysis of metagenomic sequence data generated by the 454 Life Sciences sequencing platform. The server, which is available here, generates phylogenetic and functional summaries of genomes by comparing the sequence data against protein and nucleotide databases. Researchers can upload data sets in the file format generated by the GS FLX instrument, either as raw reads or assembled contigs.

Sequin version 9.00 for Macintosh, PC/MS Windows, and Unix is available from the National Center for Biotechnology Information ftp site here. The software, a tool for uploading entries into nucleotide sequence databases, has been updated to comply with the latest version of the International Nucleotide Sequence Database Collaboration Feature Documentation.

COSMIC release 40, the Catalogue of Somatic Mutations in Cancer, is available here. The new version includes an update of existing genes, totaling almost 3,000 new mutations, as well as three additional genes that were recently identified as causes of cancer.

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.