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Downloads and Upgrades: Pacific Biosciences, Ensembl 73, Rancho Hosted TranSMART service, and more.


Pacific Biosciences has released a version of the Arabidopsis thaliana genome generated using its sequencing technology.

The complete and polished genome assemblies are available for download from the company's developer network site, along with the files necessary to submit a job with Celera assembler.

Rancho Biosciences said this week that customers can now access and use its hosted version of the TranSMART platform.

Through the Rancho Hosted TranSMART service, customers can test drive TranSMART before deciding to adopt it internally. They can also opt to use the hosted solution to support collaborations with pharmaceutical companies and academic partners. Rancho is also building related tools and additional functionality that it plans to make publically available.

Ensembl release 73 is available here.

This release includes updated patches for the human assembly, two new species — Flycatcher Ficedulla albicollis and Duck Anas platyrhynchos — and a new search engine among other changes.

SoftGenetics has added a replicate comparison tool added to GeneMarker, its genotype analysis software.

According to the company, the tool lets users automatically compare multiple replicates of their samples thus lessening the impact of allele dropout and other common sequencing artifacts and enabling users to more confidently call consensus genotypes. The company also noted that since it is incorporated into GeneMarker users now have a single platform for both genotyping and comparing replicates which should help save time and reduce errors associated with data transfer.

Exiqon, a supplier of gene expression analysis products, this week launched a bioinformatics application for its LNA longRNA GapmeR product line that lets users design antisense oligonucleotides that can inhibit mRNA and lncRNA.

The software provides users with a ranked list of designs to choose from, and it takes into account performance parameters such as LNA spiking pattern, target accessibility, secondary structures and potential off-targets based on searches against several gene databases such as Ensembl.

The Scan

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.

Lupus Heterogeneity Highlighted With Single-Cell Transcriptomes

Using single-cell RNA sequencing, researchers in Nature Communications tracked down immune and non-immune cell differences between discoid lupus erythematosus and systemic lupus erythematosus.

Rare Disease Clues Gleaned From Mobile Element Insertions in Exome Sequences

With an approach called MELT, researchers in the European Journal of Human Genetics uncovered mobile element insertions in exomes from 3,232 individuals with or without developmental or neurological abnormalities.

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.