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SoftGenetics has made available reference whole genomes for use with its NextGene second generation sequence analysis software. The company currently offers human, mouse, and rat genomes in both base space, for use with data from the Illumina Genome Analyzer and the 454 Genome Sequencer FLX, and in color space for use with the Applied Biosystems SOLiD system. It plans to add maize and bovine genomes in the near future.

The current version of NextGene also includes a whole genome builder, which allows users to construct a completely annotated reference of any species for use with the software.

The reference genome annotation includes gene name, chromosome position, reference nucleotide, reported variants, amino acid sequence, dbSNP identification, coding sequence and mRNA regions, as well as a link to dbSNP following data processing with NextGene.

The US Department of Energy Joint Genome Institute has released the Integrated Microbial Genomes system 2.9, available here. IMG is a community resource for comparative analysis and annotation of publicly available genomes from three domains of life in an integrated context. The new version contains more than one million new genes as well as certain user interface extensions. A notable new feature is the inclusion of protein expression data from a recent Arthrobacter chlorophenolicus study and tools for examining these data.

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.