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Ensembl, BioWorks 3.0, DeNovoX, OSCAR, Genquire


The Ensembl project of the Sanger Institute and the European Bioinformatics Institute has released version 4.28.1 of its human genome browser at The new release is based on the latest NCBI assembly, build 28. It contains 24,179 annotated genes, 92 percent of known genes. New features include a view of the syntenous regions of mouse across human chromosomes or vice-versa. In addition, the front page has been changed from being human-centric to multi-species in anticipation of several new vertebrate genomes over the next year.


Thermo Finnigan, a Thermo Electron business based in San Jose, Calif., has introduced two new software tools: the BioWorks 3.0 software suite, a technology platform based on the company’s TurboSequest protein identification software, and DeNovoX, a de novo sequencing software program.

BioWorks 3.0 includes an enhanced version of TurboSequest, an updated database manager, and new Pepmatch and Pepmatch tools for annotating spectral plots and chromatograms. Another new tool in the suite is Xpress, a quantitation tool that automates the differential expression of proteins.

DeNovoX can determine complete or partial amino acid sequences of unknown peptides of up to 14 amino acids by interpreting full scan MS/MS spectra, according to Thermo Finnigan. It was developed in cooperation with Jesus Vasquez, who leads the Protein Chemistry and Proteomics Laboratory at the Centro de Biologia Molecular Severo Ochoa at the Universidad Autonoma of Madrid.


The Open Cluster Group, an informal organization that supports a common base platform for cluster computing, has released version 1.2.1 of its OSCAR (Open Source Cluster Applications Resources) software package for configuring and maintaining a Linux cluster. The software is available for download at

OCG members are IBM, Intel, Oak Ridge National Laboratory, the University of Illinois’ National Center for Supercomputing Applications, Indiana University, Dell, SGI, and MSC Software.


Genquire 3.02, a genome browser and annotation tool, is available from the bioinformatics group at the National Research Council of Canada at: Genquire.

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