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

Bastiaan A. van den Berg, Marcel J T Reinders, J. Roubos, Dick de Ridder

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish
Article number93
JournalBMC Bioinformatics
Volume15
Issue number1
DOIs
Publication statusPublished - Mar 31 2014

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Protein Classification
Web-based
Proteins
Protein
Classifiers
Software
Classifier
Software Tools
Amino acids
Amino Acids
Spices
Data visualization
Data Visualization
Solubility
Amino Acid Sequence
Helix
Fungi
Yeast
Feature Extraction
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Keywords

  • Data visualization and exploration
  • Protein classification
  • Protein feature extraction
  • Sequence-based

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

SPiCE : A web-based tool for sequence-based protein classification and exploration. / van den Berg, Bastiaan A.; Reinders, Marcel J T; Roubos, J.; Ridder, Dick de.

In: BMC Bioinformatics, Vol. 15, No. 1, 93, 31.03.2014.

Research output: Contribution to journalArticle

van den Berg, Bastiaan A. ; Reinders, Marcel J T ; Roubos, J. ; Ridder, Dick de. / SPiCE : A web-based tool for sequence-based protein classification and exploration. In: BMC Bioinformatics. 2014 ; Vol. 15, No. 1.
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