Bioprocess modeling and optimization: Fed-batch clavulanic acid production by streptomyces clavuligerus

Applied Science

SPiCE: A web-based tool for sequence-based protein classification and exploration

Background Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software tools are available for both feature extraction and classifier construction, their application is not straightforward, requiring users to install various packages and to convert data into different formats. This lack of easily accessible software hampers quick, explorative use of sequence-based classification techniques by biologists. Results We have developed the web-based software tool SPiCE for exploring sequence-based features of proteins in predefined classes. It offers data upload/download, sequence-based feature calculation, data visualization and protein classifier construction and testing in a single integrated, interactive environment. To illustrate its use, two example datasets are included showing the identification of differences in amino acid composition between proteins yielding low and high production levels in fungi and low and high expression levels in yeast, respectively. Conclusions SPiCE is an easy-to-use online tool for extracting and exploring sequence-based features of sets of proteins, allowing non-experts to apply advanced classification techniques. The tool is available at http://helix.ewi.tudelft.nl/spice.Intelligent SystemsElectrical Engineering, Mathematics and Computer Scienc

Proposal for an enzyme redesign method to improve production rates in Aspergillus niger

Pattern Recognition and Bioinformatic

Relating sequence properties to protein secretion

Aspergillus niger is widely used for industrial enzyme production. Knowledge on high-level protein secretion could be useful to improve production rates. We used sequencebased classification methods to identify important propertiesfor successful high-level secretion, which will be used to redesign proteins for improved secretion.Pattern Recognition and Bioinformatic