TranSyT, an innovative framework for identifying transport systems
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/77189 |
Resumo: | 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. |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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TranSyT, an innovative framework for identifying transport systemsThe 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/publishedVersionCold Spring Harbor LaboratoryUniversidade do MinhoLagoa, Davide Rafael SantosFaria, José P.Liu, FilipeCunha, Emanuel RodriguesHenry, Christopher S.Dias, Oscar2021-04-302021-04-30T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/77189engLagoa, D.; Faria, José P.; Liu, Filipe; Cunha, Emanuel; Henry, Christopher S.; Dias, Oscar, TranSyT, an innovative framework for identifying transport systems. bioRxiv - the Preprint Server for Biology, 202110.1101/2021.04.29.441738https://www.biorxiv.org/info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:13:49Zoai:repositorium.sdum.uminho.pt:1822/77189Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:05:59.954648Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
TranSyT, an innovative framework for identifying transport systems |
title |
TranSyT, an innovative framework for identifying transport systems |
spellingShingle |
TranSyT, an innovative framework for identifying transport systems Lagoa, Davide Rafael Santos |
title_short |
TranSyT, an innovative framework for identifying transport systems |
title_full |
TranSyT, an innovative framework for identifying transport systems |
title_fullStr |
TranSyT, an innovative framework for identifying transport systems |
title_full_unstemmed |
TranSyT, an innovative framework for identifying transport systems |
title_sort |
TranSyT, an innovative framework for identifying transport systems |
author |
Lagoa, Davide Rafael Santos |
author_facet |
Lagoa, Davide Rafael Santos Faria, José P. Liu, Filipe Cunha, Emanuel Rodrigues Henry, Christopher S. Dias, Oscar |
author_role |
author |
author2 |
Faria, José P. Liu, Filipe Cunha, Emanuel Rodrigues Henry, Christopher S. Dias, Oscar |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Lagoa, Davide Rafael Santos Faria, José P. Liu, Filipe Cunha, Emanuel Rodrigues Henry, Christopher S. Dias, Oscar |
description |
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. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-04-30 2021-04-30T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/77189 |
url |
http://hdl.handle.net/1822/77189 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Lagoa, D.; Faria, José P.; Liu, Filipe; Cunha, Emanuel; Henry, Christopher S.; Dias, Oscar, TranSyT, an innovative framework for identifying transport systems. bioRxiv - the Preprint Server for Biology, 2021 10.1101/2021.04.29.441738 https://www.biorxiv.org/ |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Cold Spring Harbor Laboratory |
publisher.none.fl_str_mv |
Cold Spring Harbor Laboratory |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799132472976343040 |