An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms

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dc.contributor.author Reyes-Prieto, Mariana
dc.contributor.author Vargas-Chávez, Carlos
dc.contributor.author Llabrés, Mercè
dc.contributor.author Palmer, Pere
dc.contributor.author Latorre, Amparo
dc.contributor.author Moya, Andrés
dc.date.accessioned 2020-03-19T07:55:17Z
dc.date.available 2020-03-19T07:55:17Z
dc.identifier.uri http://hdl.handle.net/11201/151072
dc.description.abstract [eng] The Symbiotic Genomes Database (SymGenDB; http://symbiogenomesdb.uv.es/) is a public resource of manually curated associations between organisms involved in symbiotic relationships, maintaining a catalog of completely sequenced/finished bacterial genomes exclusively. It originally consisted of three modules where users could search for the bacteria involved in a specific symbiotic relationship, their genomes and their genes (including their orthologs). In this update, we present an additional module that includes a representation of the metabolic network of each organism included in the database, as Directed Acyclic Graphs (MetaDAGs). This module provides unique opportunities to explore the metabolism of each individual organism and/or to evaluate the shared and joint metabolic capabilities of the organisms of the same genera included in our listing, allowing users to construct predictive analyses of metabolic associations and complementation between systems. We also report a ~25% increase in manually curated content in the database, i.e. bacterial genomes and their associations, with a final count of 2328 bacterial genomes associated to 498 hosts. We describe new querying possibilities for all the modules, as well as new display features for the MetaDAGs module, providing a relevant range of content and utility. This update continues to improve SymGenDB and can help elucidate the mechanisms by which organisms depend on each other.
dc.format application/pdf
dc.relation.isformatof Reproducció del document publicat a: https://doi.org/10.1093/database/baz160
dc.relation.ispartof Database-The Journal Of Biological Databases And Curation, 2020, vol. 2020, p. 1-7
dc.rights cc-by (c) Reyes-Prieto, Mariana et al., 2020
dc.rights.uri http://creativecommons.org/licenses/by/3.0/es
dc.subject.classification 575 - Genètica general. Citogenètica general. Immunogenètica. Evolució. Filogènia
dc.subject.classification 51 - Matemàtiques
dc.subject.other 575 - General genetics. General cytogenetics Immunogenetics. Evolution. Phylogeny
dc.subject.other 51 - Mathematics
dc.title An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms
dc.type info:eu-repo/semantics/article
dc.type info:eu-repo/semantics/publishedVersion
dc.date.updated 2020-03-19T07:55:18Z
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.identifier.doi https://doi.org/10.1093/database/baz160


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cc-by (c) Reyes-Prieto, Mariana et al., 2020 Except where otherwise noted, this item's license is described as cc-by (c) Reyes-Prieto, Mariana et al., 2020