Thomas Hütter1, Maximilian H Ganser2, Manuel Kocher3, Merima Halkic3, Sabine Agatha2, Nikolaus Augsten3. 1. Department of Computer Sciences, University of Salzburg, Jakob-Haringer-Straße 2a, Salzburg, 5020, Austria. thomas.huetter@sbg.ac.at. 2. Department of Biosciences, University of Salzburg, Hellbrunnerstraße 34, Salzburg, 5020, Austria. 3. Department of Computer Sciences, University of Salzburg, Jakob-Haringer-Straße 2a, Salzburg, 5020, Austria.
Abstract
BACKGROUND: Molecular characters have been added in integrative taxonomic approaches in recent years. Nevertheless, taxon diagnoses are still widely restricted to morphological characters. The inclusion of molecular characters into taxon diagnoses is not only hampered by problems, such as their definition and the designation of their positions in a reference alignment, but also by the technical effort. RESULTS: DeSignate is a tool for character-based taxon diagnoses that includes a novel ranking scheme. It detects and classifies individual and combined signature characters (diagnostic molecular characters) based on so-called character state vectors. An intuitive web application guides the user through the analysis process and provides the results at a glance. Further, formal definitions and a uniform terminology of characters are introduced. CONCLUSIONS: DeSignate facilitates the inclusion of diagnostic molecular characters and their positions to complement taxon diagnoses. Compared to previous solutions, the tool simplifies the workflow and improves reproducibility and traceability of the results. The tool is freely available as a web application at (https://designate.dbresearch.uni-salzburg.at/) and is open source (https://github.com/DatabaseGroup/DeSignate/).
BACKGROUND: Molecular characters have been added in integrative taxonomic approaches in recent years. Nevertheless, taxon diagnoses are still widely restricted to morphological characters. The inclusion of molecular characters into taxon diagnoses is not only hampered by problems, such as their definition and the designation of their positions in a reference alignment, but also by the technical effort. RESULTS: DeSignate is a tool for character-based taxon diagnoses that includes a novel ranking scheme. It detects and classifies individual and combined signature characters (diagnostic molecular characters) based on so-called character state vectors. An intuitive web application guides the user through the analysis process and provides the results at a glance. Further, formal definitions and a uniform terminology of characters are introduced. CONCLUSIONS: DeSignate facilitates the inclusion of diagnostic molecular characters and their positions to complement taxon diagnoses. Compared to previous solutions, the tool simplifies the workflow and improves reproducibility and traceability of the results. The tool is freely available as a web application at (https://designate.dbresearch.uni-salzburg.at/) and is open source (https://github.com/DatabaseGroup/DeSignate/).
Authors: Luciana F Santoferrara; Charles Bachy; Viviana A Alder; Jun Gong; Young-Ok Kim; Alessandro Saccà; Inácio D da Silva Neto; Michaela C Strüder-Kypke; Alan Warren; Dapeng Xu; Zhenzhen Yi; Sabine Agatha Journal: J Eukaryot Microbiol Date: 2016-03-02 Impact factor: 3.346