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New Products: May 17, 2011


Golden Helix has added two new methods for analyzing rare variants to its SNP & Variation Suite software package.

The methods — Combined Multivariate and Collapsing and Kernel Based Adaptive Cluster — were developed in Suzanne Leal's lab at Baylor College of Medicine and allow researchers to assess the combined effect of multiple independent rare and common sequence variants on disease phenotypes.

The National Center for Biotechnology Information has released version 47 of RefSeq, available here via FTP. The release includes genomic, transcript, and protein data available as of May 7, and includes 17,631,876 records, 12,625,466 proteins, 2,619,015 RNAs, and sequences from 12,000 different organisms. Human variation data now includes clinical and medically related variations. Additionally, the vertebrate group includes some non-coding RNA records for protein coding genes when the transcript is predicted to be subject to nonsense-mediated decay.

Convey Computer has launched its Convey GraphConstructor, software that speeds up bioinformatics algorithms used in de novo genome assembly, such as Velvet and Abyss. According to the company, the key to the software is its hybrid-core computing architecture of Intel x86 microprocessors and a field-programmable gate array-based coprocessor, which allows DNA sequence alignments and other applications to run directly in hardware.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.