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Nucleic Acids Res. 2007 Jan;35(Database issue):D445-51.

TBestDB: a taxonomically broad database of expressed sequence tags (ESTs).

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  • 1Département de Biochimie, Canadian Institute for Advanced Research, Robert-Cedergren Centre for Research in Bioinformatics and Genomics, Université de Montréal, 2900 Edouard-Montpetit, Montréal, QC, Canada H3T 1J4. eobrien@bch.unmontreal.ca

Abstract

The TBestDB database contains approximately 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@bch.umontreal.ca. The database can be queried at http://tbestdb.bcm.umontreal.ca/.

PMID:
17202165
[PubMed - indexed for MEDLINE]
PMCID:
PMC1899108
Free PMC Article

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