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Verschaffelt P, Van Thienen P, Van Den Bossche T, Van der Jeugt F, De Tender C, Martens L, Dawyndt P, Mesuere B. Unipept CLI 2.0: adding support for visualizations and functional annotations. Bioinformatics 2020; 36:4220-4221. [DOI: 10.1093/bioinformatics/btaa553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/27/2020] [Accepted: 05/28/2020] [Indexed: 11/12/2022] Open
Abstract
Abstract
Summary
Unipept is an ecosystem of tools developed for fast metaproteomics data-analysis consisting of a web application, a set of web services (application programming interface, API) and a command-line interface (CLI). After the successful introduction of version 4 of the Unipept web application, we here introduce version 2.0 of the API and CLI. Next to the existing taxonomic analysis, version 2.0 of the API and CLI provides access to Unipept’s powerful functional analysis for metaproteomics samples. The functional analysis pipeline supports retrieval of Enzyme Commission numbers, Gene Ontology terms and InterPro entries for the individual peptides in a metaproteomics sample. This paves the way for other applications and developers to integrate these new information sources into their data processing pipelines, which greatly increases insight into the functions performed by the organisms in a specific environment. Both the API and CLI have also been expanded with the ability to render interactive visualizations from a list of taxon ids. These visualizations are automatically made available on a dedicated website and can easily be shared by users.
Availability and implementation
The API is available at http://api.unipept.ugent.be. Information regarding the CLI can be found at https://unipept.ugent.be/clidocs. Both interfaces are freely available and open-source under the MIT license.
Contact
pieter.verschaffelt@ugent.be
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pieter Verschaffelt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
- VIB – UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Philippe Van Thienen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
| | - Tim Van Den Bossche
- VIB – UGent Center for Medical Biotechnology, Ghent, Belgium
- CompOmics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Felix Van der Jeugt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
| | - Caroline De Tender
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Merelbeke 9820, Belgium
| | - Lennart Martens
- VIB – UGent Center for Medical Biotechnology, Ghent, Belgium
- CompOmics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium
- VIB – UGent Center for Medical Biotechnology, Ghent, Belgium
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