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

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

Van den Berg, B.A.
Reinders, M.J.
Roubos, J.A.
De Ridder, D.

Electrical Engineering, Mathematics and Computer Science

Intelligent Systems

2014-03-31

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.

sequence-based
data visualization and exploration
protein feature extraction
protein classification
OA-Fund TU Delft

http://resolver.tudelft.nl/uuid:ea7e9c1b-abfa-4575-901a-6b5a83a49b44

https://doi.org/10.1186/1471-2105-15-93

BioMed Central

1471-2105

http://www.biomedcentral.com/1471-2105/15/93

BMC Bioinformatics, 15, 2014

Institutional Repository

journal article

© 2014 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution License(http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.