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Database Commons - dbWFA

dbWFA

Citations: 2

z-index 0.08

Short name dbWFA
Full name Database of Wheat Functional Annotation
Description dbWFA is a web-based database for functional annotation of Triticum aestivum transcripts.
URL https://urgi.versailles.inra.fr/dbWFA/
Year founded 2013
Last update & version NA    v1.0
Availability Free to all users
University/Institution hosted INRA
Address 5 Chemin de Beaulieu,Clermont-Ferrand,F-63 039 Cedex 2,France
City Clermont-Ferrand
Province/State
Country/Region France
Contact name Pierre Martre
Contact email pierre.martre@clermont.inra.fr
Data type(s)
Major organism(s)
Keyword(s)
  • functional annotation
Publication(s)
  • dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts. [PMID: 23660284]

    Jonathan Vincent, Zhanwu Dai, Catherine Ravel, Frédéric Choulet, Said Mouzeyar, M Fouad Bouzidi, Marie Agier, Pierre Martre
    Database : the journal of biological databases and curation 2013:2013
    2 Citations (Google Scholar as of 2016-02-28)

    Abstract: The functional annotation of genes based on sequence homology with genes from model species genomes is time-consuming because it is necessary to mine several unrelated databases. The aim of the present work was to develop a functional annotation database for common wheat Triticum aestivum (L.). The database, named dbWFA, is based on the reference NCBI UniGene set, an expressed gene catalogue built by expressed sequence tag clustering, and on full-length coding sequences retrieved from the TriFLDB database. Information from good-quality heterogeneous sources, including annotations for model plant species Arabidopsis thaliana (L.) Heynh. and Oryza sativa L., was gathered and linked to T. aestivum sequences through BLAST-based homology searches. Even though the complexity of the transcriptome cannot yet be fully appreciated, we developed a tool to easily and promptly obtain information from multiple functional annotation systems (Gene Ontology, MapMan bin codes, MIPS Functional Categories, PlantCyc pathway reactions and TAIR gene families). The use of dbWFA is illustrated here with several query examples. We were able to assign a putative function to 45% of the UniGenes and 81% of the full-length coding sequences from TriFLDB. Moreover, comparison of the annotation of the whole T. aestivum UniGene set along with curated annotations of the two model species assessed the accuracy of the annotation provided by dbWFA. To further illustrate the use of dbWFA, genes specifically expressed during the early cell division or late storage polymer accumulation phases of T. aestivum grain development were identified using a clustering analysis and then annotated using dbWFA. The annotation of these two sets of genes was consistent with previous analyses of T. aestivum grain transcriptomes and proteomes. Database URL: urgi.versailles.inra.fr/dbWFA/

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Tags

DNA Expression
Triticum aestivum
functional annotation

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Jian Sang [2016-04-04]
    • Jian Sang [2015-12-06]
    • Jian Sang [2015-06-26]
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