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GenomeCast, GenomeQuest GeneRef Max, mpiBlast 1.3.0, Ensembl, UCSC Human Genome Browser, Isentris, Quantian, FieldScreen

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Gene-IT has launched two new products: GenomeCast and GenomeQuest GeneRef Max. GenomeCast is a “genomic broadcast network” that automatically downloads content from worldwide sequence repositories and more than 9.6 million patented sequences. The information is cross-referenced and indexed before being broadcast directly to customer servers. GenomeQuest GeneRef Max cross-references microarray probe sets with more than 266,000 gene transcripts from six public data sources and millions of patent sequence records, and is available for distribution over GenomeCast, Gene-IT said.


mpiBlast 1.3.0 is available from Los Alamos National Laboratory at http://mpiblast.lanl.gov. The release includes several enhancements, including use of the latest NCBI Toolbox; E-value scores that are identical to scores reported by NCBI Blast; and database and results pipelining to speed up the database distribution and reduce memory requirements for large query sets.


Ensembl has released a preliminary assembly for the Monodelphis domestica (opossum) genome at http://pre.ensembl.org/Monodelphis_domestica/. The assembly has a coverage of around 7.19X, and spans 3.6 billion bases (including gaps).


The University of California Santa Cruz Genome Bioinformatics Group has released the SNP annotation track for the Build 35 (hg17) UCSC Human Genome Browser (http://genome.ucsc.edu). The SNP data were obtained from dbSNP Build 123. Users now have the ability to filter the SNP data based on validation status, functional class, variant class, average heterozygosity, and other features.


Elsevier MDL has begun shipping its Isentris suite of products, the successor to MDL’s ISIS platform. Isentris consists of four products: the MDL Base user interface, the MDL Draw chemical drawing software, the MDL Core Interface middle tier, and MDL Direct chemical data cartridges for molecules and reactions.


Quantian, an extension of the Knoppix Linux distribution tailored for numerical and quantitative analysis, is available at http://dirk.eddelbuettel.com/quantian.html. It includes a complete installation of BioConductor, BioPerl, EMBOSS, and other scientific applications and visualization tools.


Cresset BioMolecular Discovery has launched FieldScreen, a software package that selects leads for targets based on electrostatic, steric, and hydrophobic molecular fields rather than molecular structure. According to the company, the software can find novel hits by screening just a few hundred compounds rather than hundreds of thousands.

 

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The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

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.