Open Access Highly Accessed Software

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

Bastiaan A van den Berg134*, Marcel JT Reinders134, Johannes A Roubos23 and Dick de Ridder134

Author Affiliations

1 Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628CD, Delft, The Netherlands

2 , DSM Biotechnology Center, Delft, The Netherlands

3 , Netherlands Bioinformatics Centre, Nijmegen, The Netherlands

4 , Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands

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BMC Bioinformatics 2014, 15:93  doi:10.1186/1471-2105-15-93

Published: 31 March 2014

Abstract

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 webcite.

Keywords:
Sequence-based; Data visualization and exploration; Protein feature extraction; Protein classification