Genome-scale metabolic reconstruction software tools | Metabolic engineering data analysis
Reconstructing a metabolic network consists in drafting the list of the biochemical reactions that an organism can carry out together with information on cellular boundaries, a biomass assembly reaction, and exchange fluxes with the external environment. Building up models able to represent the different functional cellular states is universally recognized as a tricky task that requires intensive manual effort and much additional information besides genome sequence.
Allows management, analysis, simulation and visualization of integrated collections of genome, pathway and regulatory data. Pathway Tools is a bioinformatics software environment around a type of model-organism database called Pathway/Genome Database (PGDB). The software can manipulate genome data, metabolic networks and regulatory networks. For each datatype, it provides query, visualization, editing and analysis functions. It also provides visual tools for analysis of omics data sets, and tools for the analysis of biological networks.
Enables users to reconstruct genome-scale metabolic models for any organism that has its genome sequenced. merlin is composed of two main modules, (1) one developed specifically to help on the genome annotation stage with dedicated tools and graphical user interfaces (GUIs), and (2) the other oriented to the remaining stages. The software also provides tools for curating the model. Triage, a tool for identifying the metabolites transported by each transmembrane protein and its transporter family is included in merlin.
Allows users to reconstruct, analyze, simulate and visualize genome-scale metabolic models (GEMs). RAVEN Toolbox permits users to input GEM(s) for one or more template organisms, their corresponding protein sequences, and protein sequences of the target organism. A GEM for target organism is then constructed based on orthology between the protein sequences of target organism and the organisms of template models. Some of its functionalities are also available through the browser-based GUI BioMet Toolbox.
Serves for simultaneous genome-scale metabolic reconstruction of multiple related species that leverages on the growing availability of sequenced genomes. CoReCo is a comparative metabolic reconstruction framework that reconstructs gapless metabolic models for a large number of fungal species. It allows users to annotate complete genomes to reconstruct genome-scale metabolic networks.
Allows users to construct context-specific models in an automated, deterministic, and high-throughput fashion. mCADRE emphasizes the inclusion of a high-confidence core set of reactions from a generic genome-scale model based on tissue-specific expression evidence. This tool assists users to build tissue specific metabolic models in a high-throughput manner.
Represents a genome-scale metabolic network model. AraGEM covers primary metabolism for a compartmentalized plant cell that rests on the Arabidopsis genome. This tool is able to predict classical photorespiratory cycle. It is useful for in silico functional analysis and to obtain hypotheses for working about plant metabolism.