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Downloads and Upgrades: Apr 22, 2011


The Genome Browser team at the University of California, Santa Cruz, has released a version of the sheep genome.

The assembly is based on 3X sequence coverage and includes 27 chromosomes and a mitochondrial sequence for a total sequence length of 2,860,512,983 bases.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the downloads page.

This week, the National Center for Biotechnology Information released four tracks derived from dbSNP build 132.

The new tracks contain additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options in the Genome Browser.

Ensembl 62 is available here.

The latest release includes data from human, mouse, and gibbon as well as support for the BigWig format.

Release 9 of Ensembl Genomes is also available.

The new version includes software migration to Ensembl 62 as well as new protist, fungi, metazoan, and plant genomes.


BioModels version 19 is available here.

The latest release includes 69 new models and lets users distribute models with related files as well as modifications to the underlying filesystem structure to improve performance. The public version of the database now contains 326 models in the curated branch and 373 in the non-curated branch.

Velvet 1.1.03 is available here.

The latest release includes several bug fixes and updates to the manual among other changes.

LabKey Software has released LabKey Server 11.1.
The latest release includes enhancements to assay data management, new presentation and development tools, and expanded scripting capabilities.

This week, Schrödinger launched the latest version of its computational drug design platform, Schrödinger Suite 2011.

In addition to improvements in usability and performance, the release includes updates to all products, including changes to visualization and automation tools; protein modeling and refinement tools; ligand-based and pharmacophore modeling tools; and molecular modeling and simulation tools, among others.

This week, DNAstar launched Lasergene 9, a platform that combines DNAstar’s separate software components — Lasergene Navigator, Lasergene Core Suite, SeqMan NGen, ArrayStar, QSeq, GenVision, and Protean 3D —into one integrated package .

The platform provides software tools for applications such as primer design, sequence assembly, pairwise and multiple sequence alignments, gene finding, sequence editing, annotation, plasmid map creation, genome mapping, microarray alignment and analysis, next-generation sequence assembly and analysis, and macromolecular structure, motion, and function.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.