Pheromone-Directed Seeker (PhDSeeker) is a bio-inspired algorithm for synthesizing linear and branched metabolic pathways. It allows to relate several compounds simultaneously, ensuring the availability of substrates for every reaction in the solution.
This web–demo allows to use PhDSeeker similarly as the desktop version. It requires four files as input:
- Reactions file: List of reactions to be used for synthesizing a metabolic pathway.
- Enzymes file (optional): List of enzymes catalyzing each reaction.
- Compound names file (optional): Compound names to translate codes into names. For example, KEGG code “C00001” corresponds to “water”.
- Settings file: Configuration parameters of the algorithm.
An example for each file is provided with the web–demo. As outputs, PhDSeeker returns three files:
- Summary: Text file containing the detail of the experimental settings used and the list of reactions comprising the solution found.
- History: Text file with the list of pathways found along the search. The reactions that comprise each pathway are detailed.
- Pathway: Downloadable file with the solution found represented as an interactive graph (its elements can be re-arranged manually online). An interactive version is also displayed at bottom of this page.
Contact: Matias Gerard