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BioBoost, MatBase, AurScope Kinase Knowledge, Geneious Pro 2.0, ProtoNet 4.5, Ensembl 40, UCSC Genome Browser, MDL Registration

Progeniq has released a new version of its BioBoost FPGA-based bioinformatics accelerator that runs on Mac OS X version 10.4. The company said that BioBoost can run pairwise and multiple sequence alignment on Intel Macs up to 50 times faster than a typical processor.

Genomatix Software has released MatBase, a knowledgebase of transcription factor binding sites and protein binding domains, related literature, and more than 27,000 known transcription factors.

Aureus Pharma has released the AurScope Kinase Knowledge database, which includes biological activity data on kinases that has been mined from the scientific literature and patents.

Biomatters has released Geneious Pro 2.0. New features include an improved user interface, improved search and agents, a public API, and ClustalW alignments.

ProtoNet 4.5, an automated classification system for protein sequences based on hierarchical clustering, is available from HebrewUniversity at The new version includes the classification of all proteins in SwissProt and supports TrEMBL entries.

Ensembl 40 is available at New features include improved gene builds for low-coverage genomes, such as elephant, armadillo, tenerec and rabbit; a new display for gene-level trees; and full gene builds for rhesus macaque and stickleback.

The Genome Bioinformatics Group at the University of California, Santa Cruz, has released the latest draft assembly of the opossum (Monodelphis domestica) genome through the UCSC Genome Browser. This release was sequenced and assembled by The Broad Institute, and has approximately 6.5X coverage with an assembly length of nearly
3.61 billion bp, including gaps. The sequence and annotation data can be downloaded from the FTP server at or the downloads page at

Elsevier MDL has launched MDL Registration, an application for building and managing compound registries. MDL Registration is built on the MDL Isentris system and automatically verifies drawing conventions, normalizes structure data, and checks for uniqueness before assigning corporate IDs and storing submitted substances in the database.

Filed under

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.