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GenBank, UCSC Genome Bioinformatics, ProteinScope 0.8.9, MiraiBio, Predictive Patterns Software

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GenBank release 137.0 is now available from NCBI at ftp://ftp.ncbi.nih.gov/. The release contains 33,865,022,251 base pairs and 27,213,748 entries, up by 1,336,772,956 base pairs and 1,620,883 sequence records from the June 136.0 release. Uncompressed, the 137.0 flat files require about 112 GB for the sequence files only. The ASN.1 version requires around 98 GB.

The UCSC Genome Bioinformatics group has released a browser and Blat server for the “zoo” data analyzed by the NIH Intramural Sequencing Center Comparative Sequencing Program. The browser displays sequence and annotations for a region containing 10 previously identified genes in 13 vertebrate species. The data may be accessed by the “zoo” option from the genome list at (http://genome. ucsc.edu/cgi-bin/hgGateway).

ProteinScope 0.8.9, a free viewer for Protein Data Bank files, is available for Windows at http://www.proteinscope.com. New features include the ability to export PDB records to Excel spreadsheets.

MiraiBio has launched its DNASIS GeneIndex service, an Internet-based data integration and query service that retrieves information from 23 publicly available biological databases. The service also offers GETA (Generic Engine for Transportable Association), a text-mining engine developed originally by Hitachi Central Research and IPA (Information Technology Promotion Agency, Japan).

Predictive Patterns Software has released GeneLinker Gold and Platinum 4.0. The new version includes meta-scripting, which allows multiple scripts to be chained together. Other features include import of native Excel files and experiment scripting.

 

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The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.