TranSyT, an innovative framework for identifying transport systems
| Autor: | Lagoa, Davide Rafael Santos, Faria, José P., Liu, Filipe, Cunha, Emanuel Rodrigues, Henry, Christopher S., Dias, Oscar |
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| Přispěvatelé: | Universidade do Minho |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Popis: | The importance and rate of development of genome-scale metabolic models have been growing for the last years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGEs release, software development for automatic integration of transport reactions into models has stalled. Here we present the Transport Systems Tracker (TranSyT), the next iteration of TRIAGE. Unlike its predecessor, TranSyT does not rely on manual curation to expand its internal database, derived from highly-curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporters families, transport proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase. This study was supported by the Portuguese Foundation for Science and Technology(FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. This work is supported by the Office of Biological and Environmental Research’s Genomic Science program within the US Department of Energy Office of Science, under award numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE AC05-00OR22725, and DE-AC02-98CH10886. info:eu-repo/semantics/publishedVersion |
| Databáze: | OpenAIRE |
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