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Related Experiment Video

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Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

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CleanEST: a database of cleansed EST libraries.

Byungwook Lee¹, Gwangsik Shin

¹Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea. bulee@kribb.re.kr

Nucleic Acids Research

|October 4, 2008

Summary

CleanEST is a new database server that classifies and removes contaminants from expressed sequence tag (EST) libraries. This improves the accuracy of gene discovery and exon-intron structure verification using dbEST data.

Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Expressed Sequence Tag (EST) databases like dbEST are crucial for gene discovery and structural analysis.
Inconsistent library descriptions and sequence contamination hinder the effective use of dbEST data.

Purpose of the Study:

To introduce CleanEST, a novel database server designed to classify and cleanse dbEST libraries.
To enhance the reliability and usability of EST sequences for research applications.

Main Methods:

Classification of dbEST libraries by species, sequencing center, and human anatomical/pathological systems (using eVOC ontologies).
Development of a 'pre-cleansed' sequence set by aligning ESTs against known contaminants (UniVec, E. coli, mitochondria, chloroplast).
Implementation of an automatic 'user-cleansed' pipeline for on-the-fly sequence cleaning based on user-selected options.

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Main Results:

CleanEST provides systematically classified dbEST libraries.
Two distinct sets of cleansed sequences ('pre-cleansed' and 'user-cleansed') are offered.
The database is updated monthly to ensure current data.

Conclusions:

CleanEST addresses key limitations in dbEST data quality by classifying libraries and removing contaminants.
The server facilitates more accurate gene discovery and structural verification.
CleanEST offers a valuable resource for researchers utilizing EST data.