CleanEST: a database of cleansed EST libraries

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Title
CleanEST: a database of cleansed EST libraries
Author(s)
ByungWook Lee; GwangSik Shin
Bibliographic Citation
Nucleic Acids Research, vol. 37, no. D, pp. D686-D689
Publication Year
2009
Abstract
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.
ISSN
0305-1048
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/nar/gkn648
Type
Article
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1. Journal Articles > Journal Articles
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