swMATH ID: 35556
Software Authors: Roland Schwarz, Patrick Musch, Axel von Kamp, Bernd Engels, Heiner Schirmer, Stefan Schuster, Thomas Dandekar
Description: YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. Results: YANA features a platform-independent, dedicated toolbox for metabolic networks with a graphical user interface to calculate (integrating METATOOL), edit (including support for the SBML format), visualize, centralize, and compare elementary flux modes. Further, YANA calculates expected flux distributions for a given Elementary Mode (EM) activity pattern and vice versa. Moreover, a dissection algorithm, a centralization algorithm, and an average diameter routine can be used to simplify and analyze complex networks. Proteomics or gene expression data give a rough indication of some individual enzyme activities, whereas the complete flux distribution in the network is often not known. As such data are noisy, YANA features a fast evolutionary algorithm (EA) for the prediction of EM activities with minimum error, including alerts for inconsistent experimental data. We offer the possibility to include further known constraints (e.g. growth constraints) in the EA calculation process. The redox metabolism around glutathione reductase serves as an illustration example. All software and documentation are available for download at http://yana.bioapps.biozentrum.uni-wuerzburg.de. Conclusion: A graphical toolbox and an editor for METATOOL as well as a series of additional routines for metabolic network analyses constitute a new user-friendly software for such efforts.
Homepage: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-135
Related Software: Metatool; FluxAnalyzer; efmtool; FFCA
Referenced in: 4 Publications

Referenced in 1 Serial

4 Journal of Theoretical Biology

Referencing Publications by Year