ArticleNucleic acids research2009
CleanEST: a database of cleansed EST libraries.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Universality of the DNA methylation codes in Eucaryotes.Scientific reports · 2019Article
- Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Article
- Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Article
- EuroPineDB: a high-coverage web database for maritime pine transcriptome.BMC genomics · 2011Article
- Protein comparison at the domain architecture level.BMC bioinformatics · 2009Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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. The server is available at http://cleanest.kobic.re.kr/ and the database is updated monthly.
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