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.