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

• Published in: BMC bioinformatics Vol. 15; no. 1; p. 93
• Main Authors: van den Berg, Bastiaan A, Reinders, Marcel J T, Roubos, Johannes A, de Ridder, Dick
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 31-03-2014; BioMed Central
• Subjects: Algorithms; Amino Acid Sequence; Aspergillus niger; Bioinformatics; Classification; Discriminant analysis; Internet; Molecular Sequence Data; Programming languages; Protein expression; Proteins; Proteins - chemistry; Saccharomyces cerevisiae; Sequence Analysis, Protein - methods; Software; Software Design; Visualization (Computers); Yeast
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-15-93

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.
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.
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.