Publication Date:
2014-04-02
Description:
Background: Amino acid sequences and features extracted from such sequences have been used to predict manyprotein properties, such as subcellular localization or solubility, using classifier algorithms. Althoughsoftware tools are available for both feature extraction and classifier construction, their applicationis not straightforward, requiring users to install various packages and to convert data into differentformats. This lack of easily accessible software hampers quick, explorative use of sequence-basedclassification techniques by biologists. Results: We have developed the web-based software tool SPiCE for exploring sequence-based features ofproteins in predefined classes. It offers data upload/download, sequence-based feature calculation,data visualization and protein classifier construction and testing in a single integrated, interactiveenvironment. To illustrate its use, two example datasets are included showing the identification ofdifferences in amino acid composition between proteins yielding low and high production levels infungi 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 ofproteins, allowing non-experts to apply advanced classification techniques. The tool is available athttp://helix.ewi.tudelft.nl/spice.
Electronic ISSN:
1471-2105
Topics:
Biology
,
Computer Science
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