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TBestDB


NAR Molecular Biology Database Collection entry number 912
O'Brien, E.A.1, Koski, L.1, Zhang, Y.1, Yang, L.1, Wang, E., Gray, M.W.2, Burger, G.1 and Lang, B.F.1
1Center Robert-Cedergren for Bioinformatics and Genomics, Departement de Biochimie, Pavillon Roger-Gaudry, Universite de Montreal, 2900 Edouard-Montpetit, Montreal QC, H3T 1J4, Canada
2Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada

Database Description

The TBestDB (a Taxonomically Broad EST database) database contains ~370,000 clustered EST sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, consensus sequences, gene annotations and metabolic pathway predictions. Most of these ESTs have been generated by the Protist EST Program, a collaboration among six Canadian research groups. EST sequences are read from trace files up to a minimum quality cut-off, vector and linker sequence is masked, and the ESTs are clustered using phrap. The resulting consensus sequences are automatically annotated by the AutoFACT program. The datasets are automatically checked for clustering errors due to chimerism and potential cross-contamination between organisms, and suspect data are flagged in or removed from the database. Access to data deposited in TBestDB by individual users can be restricted to those users for a limited period. With this first report on TBestDB, we open the database to the research community for free processing, annotation, interspecies comparisons and GenBank submission of EST data generated in individual laboratories. For instructions on submission to TBestDB, contact tbestdb@bch.umontreal.ca. The database can be queried at http://tbestdb.bcm.umontreal.ca/.


Go to the abstract in the NAR 2007 Database Issue.
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