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Downloads and Upgrades: RefSeq 57, Ensembl 70, SBML Test Suite database, and more


The developers of the Structural Classification of Proteins, or SCOP, and ASTRAL databases have released version 1.75B of the combined resources.

The release includes bug fixes and automated classification of many new PDB files released before Nov. 20, 2012.

RefSeq 57 is now available from the National Center for Biotechnology Information via FTP.

This release incorporates genomic, transcript, and protein data available as of Jan. 8 and includes 34,158,511 records; 27,834,581 proteins; 3,267605 RNAs; and sequences from 21,415 different organisms.

The UCSC Genome Browser group has released a new browser for lamprey, Petromyzon marinus.

The whole-genome shotgun assembly was provided by the Genome Institute at Washington University. There are 25,006 scaffolds with a total size of 885,550,958 bases.

Ensembl release 70 is available here.

This release includes updates patches for human assembly, reanalyzed human bodymap data, a new regulatory build for mouse including a much broader coverage for the embryonic fibroblast build and additional data on other cell types.

The SBML Test Suite database is available here.

According to the developers, the resource publicizes software systems' support of SBML as determined by their performance on the test suite. Users can search the tool to find the test results for different software systems and developers of SBML software can submit their results for dissemination to the community.

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The Scan

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.

US Survey Data Suggests Ancestry Testing Leads Way in Awareness, Use of Genetic Testing Awareness

Although roughly three-quarters of surveyed individuals in a Genetics in Medicine study reported awareness of genetic testing, use of such tests was lower and varied with income, ancestry, and disease history.

Coral Genome Leads to Alternative Amino Acid Pathway Found in Other Non-Model Animals

An alternative cysteine biosynthesis pathway unearthed in the Acropora loripes genome subsequently turned up in sequences from non-mammalian, -nematode, or -arthropod animals, researchers report in Science Advances.

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.