Unipept CLI 2.0: adding support for visualizations and functional annotations

Pieter Verschaffelt; Philippe Van Thienen; Tim Van Den Bossche; Felix Van der Jeugt; Caroline De Tender; Lennart Martens; Peter Dawyndt; Bart Mesuere

doi:10.1093/bioinformatics/btaa553

Unipept CLI 2.0: adding support for visualizations and functional annotations

Bioinformatics. 2020 Aug 15;36(14):4220-4221. doi: 10.1093/bioinformatics/btaa553.

Authors

Pieter Verschaffelt^{1

2}, Philippe Van Thienen¹, Tim Van Den Bossche^{2

3}, Felix Van der Jeugt¹, Caroline De Tender^{1

4}, Lennart Martens^{2

3}, Peter Dawyndt¹, Bart Mesuere^{1

2}

Affiliations

¹ Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium.
² VIB - UGent Center for Medical Biotechnology, Ghent, Belgium.
³ CompOmics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
⁴ Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Merelbeke 9820, Belgium.

PMID: 32492134
DOI: 10.1093/bioinformatics/btaa553

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Data Analysis
Ecosystem*
Peptides
Software*

Substances

Peptides