Skip to main content
Premium Trial:

Request an Annual Quote

Ciphergen Biosystems, SwissProt, Protein Data Bank

Premium

Ciphergen Biosystems has released, in conjunction with Salford Systems, Biomarker Patterns Software 5.0 for the elucidation of clinically relevant protein patterns. The software is based upon a recently issued patent for finding protein patterns in mass spectra using a classification and regression tree algorithm (see PM 2-20-04). The software is intended for use with Ciphergen’s SELDI ProteinChip system. Ciphergen and Salford collaborated to create the software by modifying Salford’s existing Classification and Regression Tree procedure. Ciphergen holds exclusive rights to the technology. A new component to Biomarker Patterns Software 5.0 is an intelligent feature selection using functionality from Salford’s TreeNet algorithm. TreeNet builds a large number of small trees that each corrects the errors of its predecessors. This helps avoid the potential problem of over-trained data sets, according to Ciphergen.

The software “sets Ciphergen’s proteomics platform apart from groups that are using other pattern recognition methods without protein ID and from groups cataloguing protein IDs for literature validation in order to guess which protein will make a good assay — a classical approach which has had limited success in developing in vitro diagnostic tests over the past decades,” Martin Verhoef, president of Ciphergen’s Biosystems Division, said in a statement.


Version 43.0 of SwissProt is now available for access at the website http://www.ebi.ac.uk/sprot/. The release contains 146,720 fully annotated sequences and 54,093,154 amino acids.


The Protein Data Bank is making available a new QuickSearch keyword search feature. The new feature supports searches across the PDB archive and website static pages.

 

The Scan

Driving Malaria-Carrying Mosquitoes Down

Researchers from the UK and Italy have tested a gene drive for mosquitoes to limit the spread of malaria, NPR reports.

Office Space to Lab Space

The New York Times writes that some empty office spaces are transforming into lab spaces.

Prion Pause to Investigate

Science reports that a moratorium on prion research has been imposed at French public research institutions.

Genome Research Papers on Gut Microbe Antibiotic Response, Single-Cell RNA-Seq Clues to Metabolism, More

In Genome Research this week: gut microbial response to antibiotic treatment, approach to gauge metabolic features from single-cell RNA sequencing, and more.