ArticleBioinformatics (Oxford, England)2023
TranSyT, an innovative framework for identifying transport systems.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 12 citations in OpenAlex.
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- A diel multi-tissue genome-scale metabolic model of Vitis vinifera.PLoS computational biology · 2024Article
- Mixotrophic growth of a ubiquitous marine diatom.Science advances · 2024Article
- Transporter annotations are holding up progress in metabolic modeling.Frontiers in systems biology · 2024Article
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.PLoS computational biology · 2023Article
- TransAAP: an automated annotation pipeline for membrane transporter prediction in bacterial genomes.Microbial genomics · 2023Article
- merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models.Nucleic acids research · 2022Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe importance and rate of development of genome-scale metabolic models have been growing for the last few years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGE's release, software development for the automatic integration of transport reactions into models has stalled.
resultsHere, we present the Transport Systems Tracker (TranSyT). Unlike other transport systems annotation software, TranSyT does not rely on manual curation to expand its internal database, which is derived from highly curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporter families and 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. AVAILABILITY AND IMPLEMENTATION: TranSyT web service: https://transyt.bio.di.uminho.pt/; GitHub for the tool: https://github.com/BioSystemsUM/transyt; GitHub with examples and instructions to run TranSyT: https://github.com/ecunha1996/transyt_paper.
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