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Pheromone Directed Seeker (PhDSeeker) allows the automatic search of metabolic pathways that relate a set of specified compounds using an ant-based algorithm. The algorithm can automatically identify one of the compounds to relate as the substrate from which the other compounds must be synthesized. It also can be specified in the compounds file.
Input data:
- Reactions file: It contains the set of reactions that can be used to built a metabolic pathways.
- Compounds file: It contains the set of freely available compounds (i.e. water) and the compounds to relate.
- Settings file: It contains the configuration parameters of the algorithm.
Output data:
- Best pathway (html): Open a graphical representation of the metabolic pathway found in a new browser tab.
- Best pathway (txt): File containing the solution found, presented as an ordered list of reactions.
- All pathways (txt): File containing all the solutions found during the search, each one presented as a list of reactions, with the best solution at top.
- Additional information: File containing information of the search process.