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Downloads & Upgrades: Ensembl 65; Ensembl Genomes 12; Partek Flow and Partek Pathway; BGI-BOX

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Ensembl 65 is available here.

The release includes an assembly for the Atlantic cod (Gadus morhua); the most recent human and zebrafish manual gene annotations, and updated mouse variation data, among other additions.

Separately, release 12 of Ensembl Genomes is available here.

The release includes a migration to version 65 of the Ensembl software; operon data from Regulon DB for Escherichia coli; five new genomes; a new species, Ashbya gossypii; and manually curated annotation from a new yeast resource. It also includes the first release of Ensembl Fungi containing data from PomBase, a new resource for the fission yeast Schizosaccharomyces pombe(BI 12/2/2011), among other updates.


This week, Partek released two new software products; Partek Flow and Partek Pathway.

Partek Flow provides upstream alignment, quality assurance and control, and quantification of next-generation sequencing data, the company said.

Partek Pathway contextualizes gene relationships identified within Partek Genomics Suite, enabling users to study multiple relationships, calculate pathway enrichment, search for specific pathways and genes, and color-code them based on their p-values and fold changes. Additionally, it links to other online databases so that users can make comparisons to other research findings.


BGI has launched BGI-BOX, a cloud computing terminal server that lets non-bioinformatics experts perform data analysis in their laboratories.

The platform provides several of BGI's standard bioinformatics analysis pipelines and software, including assembly tools and genetic variation analysis software. These tools let users perform basic analysis as well as create customized solutions by selecting relevant software and adjusting specific parameters under each analysis module.

The first BGI-BOX has been implemented at China Agricultural University and BGI plans to install 50 such systems worldwide in the first quarter of 2012.


The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.