2.50
Hdl Handle:
http://hdl.handle.net/10033/338870
Title:
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics.
Authors:
Duarte, Márcia; Jauregui, Ruy; Vilchez-Vargas, Ramiro ( 0000-0002-7220-258X ) ; Junca, Howard ( 0000-0003-4546-6229 ) ; Pieper, Dietmar H
Abstract:
Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL: http://aromadeg.siona.helmholtz-hzi.de.
Affiliation:
Research group Microbial interactions and processes (MINP). Helmholtz Centre for infection research, Inhoffenstr. 7, D38124 Braunschweig, Germany.
Citation:
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics. 2014, 2014: Database (Oxford)
Journal:
Database : the journal of biological databases and curation
Issue Date:
2014
URI:
http://hdl.handle.net/10033/338870
DOI:
10.1093/database/bau118
PubMed ID:
25468931
Type:
Article
Language:
en
ISSN:
1758-0463
Appears in Collections:
publications of the research group microbial interactions and processes (MINP)

Full metadata record

DC FieldValue Language
dc.contributor.authorDuarte, Márciaen
dc.contributor.authorJauregui, Ruyen
dc.contributor.authorVilchez-Vargas, Ramiroen
dc.contributor.authorJunca, Howarden
dc.contributor.authorPieper, Dietmar Hen
dc.date.accessioned2015-01-26T15:10:42Zen
dc.date.available2015-01-26T15:10:42Zen
dc.date.issued2014en
dc.identifier.citationAromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics. 2014, 2014: Database (Oxford)en
dc.identifier.issn1758-0463en
dc.identifier.pmid25468931en
dc.identifier.doi10.1093/database/bau118en
dc.identifier.urihttp://hdl.handle.net/10033/338870en
dc.description.abstractUnderstanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL: http://aromadeg.siona.helmholtz-hzi.de.en
dc.language.isoenen
dc.titleAromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics.en
dc.typeArticleen
dc.contributor.departmentResearch group Microbial interactions and processes (MINP). Helmholtz Centre for infection research, Inhoffenstr. 7, D38124 Braunschweig, Germany.en
dc.identifier.journalDatabase : the journal of biological databases and curationen

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