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New Products: Nov 29, 2011

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Researchers from the University of California, Berkeley, and the University of Maryland have released version 1.2.0 of the transcript assembly software Cufflinks here. The new release fixes several bugs and includes accuracy and performance improvements.


The National Center for Biotechnology Information has released its Variation Reporter Tool to match variant calls with variants in dbSNP or dbVar. The new tool is available here, and will provide detailed information on known alleles for the variant call. If the variant is not present in either database it will calculate whether it has a predicted functional consequence.

The NCBI has also added human variant call format files and human genotype XML files by gene to dbSNP, available here via FTP.


Researchers from Johns Hopkins School of Public Health have released Bowtie version 2.0 for aligning sequence reads to the reference. The new release, available here, includes accuracy improvements, speed improvements, and fixes several bugs.

The Scan

Just Breathing

A new analysis suggests that most Mycobacterium tuberculosis is spread by aerosols from breathing, rather than by coughing, the New York Times reports.

Just Like This One

NPR reports that the World Health Organization has hired a South African biotech company to recreate mRNA vaccine for SARS-CoV-2 that is similar to the one developed by Moderna.

Slow Start

The Wall Street Journal reports that Biogen's Alzheimer's disease treatment had revenues for July through September that totaled $300,000.

Genome Research Papers on Cancer Chromatin, Splicing in the Thymus, Circular RNAs in Cancer

In Genome Research this week: analysis of bivalent chromatin sites, RBFOX splicing factors' role in thymic epithelial cells, and more.