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Desharky specifications


Unique identifier OMICS_04877
Name Desharky
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Alfonso Jaramillo

Publication for Desharky

Desharky citations


A review of computational tools for design and reconstruction of metabolic pathways

PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] st at each edge, RouteSearch defined an additional criterion at each edge for non-static atom lost and applied branch-and-bound search to find the best paths to minimize the loss . On the other hand, DESHARKY applied Monte Carlo method to search for reaction combinations. To find the shortest path by S matrix representation, stoichiometry-based pathway design algorithms that use MILP is the commo […]


A review of parameters and heuristics for guiding metabolic pathfinding

J Cheminform
PMCID: 5602787
PMID: 29086092
DOI: 10.1186/s13321-017-0239-6

[…] ny others require the user to select which organism or group of organisms to look at [, ]. Other methods do not require user input. In Cho et al.¬†[], enzymes are ranked based on organism specificity. DESHARKY [] limits the number of compounds that are not organism-specific to only one non-specific reactant and one non-specific product. In GEM-Path [], there is an association between reactions and […]


Development of bio based fine chemical production through synthetic bioengineering

Microb Cell Fact
PMCID: 4302092
PMID: 25494636
DOI: 10.1186/s12934-014-0173-5

[…] are identified, one can move to pathway design and optimization for microbial production of the target compound. Several computational tools are available, such as BNICE [], FMM [], RetroPath [], and DESHARKY [] and M-path [] for designing de novo metabolic pathways. These resources provide different views of metabolic pathways for microbial production that are generated using the enormous amount […]


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Desharky institution(s)
Instituto de Biologia Molecular y Celular de Plantas, CSIC, Spain

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