Nucleic Acids Research, 2007, Vol. 35, Database issue D445-D451
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)
Département de Biochimie, Canadian Institute for Advanced Research, Robert-Cedergren Centre for Research in Bioinformatics and Genomics, Pavillon Roger-Gaudry, Université de Montréal, 2900 Edouard-Montpetit, Montréal QC Canada H3T 1J4 1 Cenix BioScience, Tatzberg 47 01307 Dresden, Germany 2 Department of Biochemistry and Molecular Biology, Dalhousie University Halifax, Nova Scotia, Canada B3H 1X5
*To whom correspondence should be addressed. Tel: +1 514 343 5188; Fax: +1 514 343 2210; Email: eobrien{at}bch.unmontreal.ca
Received July 25, 2006. Revised September 11, 2006. Accepted October 1, 2006.
The TBestDB database contains 
370 000 clustered expressed sequence tag (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 using 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{at}bch.umontreal.ca. The database can be queried at http://tbestdb.bcm.umontreal.ca/.
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