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dbWFA

The search for homologous sequences and orthologs is very useful for analyzing biological sequences, especially when studying a species whose genome is still to be entirely sequenced such as wheat. Steady growth of the size of genomic database makes homologous sequences analysis very time-consuming. Moreover, the functional annotation of the genes based on their sequence homology with model species genomes requires querying unrelated databases. Expressed sequence tags and transcripts represent one of the most important sources of information in gene expression studies; however, raw sequences must be annotated before they are of value to the research community. The aim of the present work was to develop a functional annotation database dedicated to bread wheat (Triticum aestivum), gathering information about model plant species and linking them to wheat through BLAST results.


wheat_dbWFA

 

Run dbWFA

 

Reference

Jonathan Vincent, Zhanwu Dai, Catherine Ravel, Frédéric Choulet, Said Mouzeyar,
M. Fouad Bouzidi, Marie Agier and Pierre Martre dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts. Database, Vol. 2013, Article ID bat014, doi:10.1093/database/bat014

 

Database Structure and Website

The database contains information about Gene Ontologies , functional annotations , gene families and metabolic pathways . More than four million BLAST results were stored, allowing an efficient use of the database. Following the recommendation of the International Wheat Genome Sequencing Consortium (IWGSC ) for homology research, the percentages of coverage and identity is used to assign functional annotations to wheat transcripts.

The database was built so that one can use two different query’s approaches. From wheat transcripts IDs or NimbleGen gene expression array probes to putative family, ontology, function, and/or metabolic pathway through BLAST results, and vice versa. BLAST results allow one to characterize the homology and assign putative functional annotation between two sequences based on coverage and identity threshold values specified by the user.

A tool was developed by the "Integrative biology of grain composition team from INRA UMR1095 GDEC " in order to grant users with the most common queries that can be applied to the database. It includes searching for genes involved in specified metabolic pathways, functional annotations, gene ontologies or belonging to specified families. Or inversely, searching for putative annotations related to a wheat transcript or a list of wheat transcripts. Results are available as detailed web/html pages or text files.

 

dbWFA database schema

 

 

Other references:

Rodrigo A. Gutiérrez, Dennis E. Shasha, and Gloria M. Coruzzi Systems Biology for the Virtual Plant. Plant Physiol., 138:550–554, 2005.

Altschul SF, Gish W, Miller W, Myers, EW, Lipman DJ. Basic local alignment search tool. J. Mol. Biol., 215:403–410, 1990.

Romeuf I, Tessier D, Dardevet M, Branlard G, Charmet G, Ravel C. wDBTF: an integrated database resource for studying wheat transcription factor families. BMC Genomics, 11:185, 2010.

Rustenholz C, Choulet F, Laugier C, Safar J, Simkova H, Dolezel J, Magni F, Scalabrin S, Cattonaro F, Vautrin S, Bellec A, Bergès H, Feuillet C and Paux E (2011) A 3000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. Submittedfor publication.

Mewes HW, Ruepp A, Theis F, Rattei T, Walter M, Frishman D, Suhre K, Spannagl M, Mayer KF, Stümpflen V, Antonov A. MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res., 39:D220-4, 2011.

International Wheat Genome Sequencing Consortium. Guidelines for annotating wheat genomic sequences: release 1. Available at <http://www.wheatgenome.org/content/download/794/8948/file/wheat_gene_annotation_Release1-1.pdf>, 2006.

Romeuf I. Identification in silico des facteurs de transcription du blé tendre (Triticum aestivum) et mise en évidence des facteurs de transcription impliqués dans la synthèse des protéines de réserve. Ph.D. thesis, Université Blaise Pascal, Clermont-Ferrand, France, 2010.

Update: 04 Jun 2013
Creation date: 11 Aug 2011