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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.

Filed under

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.