ArticleBMC bioinformatics2014
SPiCE: a web-based tool for sequence-based protein classification and exploration.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria.Briefings in bioinformatics · 2022Article
- PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach.Viruses · 2022Article
- MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors.Briefings in bioinformatics · 2022Article
- Effective prediction of bacterial type IV secreted effectors by combined features of both C-termini and N-termini.Journal of computer-aided molecular design · 2017Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAmino 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.
resultsWe 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.
conclusionsSPiCE 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.
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Registered trials
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