title: SPiCE: a web-based tool for sequence-based protein classification and exploration.
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.
authors.affiliation: Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628CD, Delft, The Netherlands. b.a.vandenberg@tudelft.nl.
authors.forename: Bastiaan A
authors.initials: BA
authors.lastname: van den Berg
authors.forename: Marcel J T
authors.initials: MJ
authors.lastname: Reinders
authors.forename: Johannes A
authors.initials: JA
authors.lastname: Roubos
authors.forename: Dick
authors.initials: D
authors.lastname: de Ridder
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001234:Aspergillus niger; D020407:Internet; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D012441:Saccharomyces cerevisiae; D020539:Sequence Analysis, Protein / Q000379:methods*; D012985:Software Design
chemical_list: D011506:Proteins