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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

Review of Approval Process

Stat News reports the Department for Health and Human Services' Office of the Inspector General is to investigate FDA's approval of Biogen's Alzheimer's disease drug.

Not Quite Right

A new analysis has found hundreds of studies with incorrect nucleotide sequences reported in their methods, according to Nature News.

CRISPR and mRNA Together

Time magazine reports on the use of mRNA to deliver CRISPR machinery.

Nature Papers Present Smartphone Platform for DNA Diagnosis of Malaria, Mouse Lines for Epigenomic Editing

In Nature this week: a low-cost tool to detect infectious diseases like malaria, and more.