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Nucleic Acids Research Advance Access originally published online on October 2, 2008
Nucleic Acids Research 2009 37(Database issue):D686-D689; doi:10.1093/nar/gkn648
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Nucleic Acids Research, 2009, Vol. 37, Database issue D686-D689
© 2008 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.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

CleanEST: a database of cleansed EST libraries

Byungwook Lee1,2,* and Gwangsik Shin1

1Korean BioInformation Center, KRIBB, Daejeon 305-817 and 2Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Korea

*To whom correspondence should be addressed. Tel: +82 42 879 8531; Fax: +82 42 879 8519; Email: bulee{at}kribb.re.kr

Received August 5, 2008. Revised September 5, 2008. Accepted September 18, 2008.

The EST division of GenBank, dbEST, is widely used in many applications such as gene discovery and verification of exon–intron structure. However, the use of EST sequences in the dbEST libraries is often hampered by inconsistent terminology used to describe the library sources and by the presence of contaminated sequences. Here, we describe CleanEST, a novel database server that classified dbEST libraries and removes contaminants. We classified all dbEST libraries according to species and sequencing center. In addition, we further classified human EST libraries by anatomical and pathological systems according to eVOC ontologies. For each dbEST library, we provide two different cleansed sequences: ‘pre-cleansed’ and ‘user-cleansed’. To generate pre-cleansed sequences, we cleansed sequences in dbEST by alignment of EST sequences against well-known contamination sources: UniVec, Escherichia coli, mitochondria and chloroplast (for plant). To provide user-cleansed sequences, we built an automatic user-cleansing pipeline, in which sequences of a user-selected library are cleansed on-the-fly according to user-selected options. The server is available at http://cleanest.kobic.re.kr/ and the database is updated monthly.


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