DESHARKY

The software tool 'DESHARKY' is a computational framework that uses a Monte Carlo algorithm to find a metabolic pathway from a target compound by exploring a database of enzymatic reactions. It outputs a biochemical route to the host metabolism and its impact in the cellular context using mathematical models of the cell resources and metabolism. The tool provides the sequence of amino acids for the enzymes involved in the route closest phylogenetically to the considered organism.

Topic

Metabolic pathway inference

Detail

  • Operation: Sequence alignment search; Pathway prediction; Metabolic network modeling; Monte Carlo simulation; Database search; Biochemical route identification; Enzyme sequence identification; Mathematical modeling.

  • Software interface: -

  • Language: -

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: eneralitat Valenciana G.R., Spanish Ministry of Education, MIT-France program, Structural Funds ERDF; EU grant BioModularH2.

  • Input: -

  • Output: -

  • Contact: alfonso.jaramillo@polytechnique.fr

  • Collection: -

  • Maturity: Stable

Publications

  • DESHARKY: automatic design of metabolic pathways for optimal cell growth.
  • Rodrigo G, et al. DESHARKY: automatic design of metabolic pathways for optimal cell growth. DESHARKY: automatic design of metabolic pathways for optimal cell growth. 2008; 24:2554-6. doi: 10.1093/bioinformatics/btn471
  • https://doi.org/10.1093/bioinformatics/btn471
  • PMID: 18776195
  • PMC: -

Download and documentation

    Currently not available or not maintained.

< Back to DB search