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Nucleic Acids Research, 2003, Vol. 31, No. 13 3716-3719
© 2003 Oxford University Press

ESTAnnotator: a tool for high throughput EST annotation

Agnes Hotz-Wagenblatt*, Thomas Hankeln1, Peter Ernst, Karl-Heinz Glatting, Erwin R. Schmidt1 and Sándor Suhai

Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany 1 GENterprise GmbH, J.J. Becherweg 32, D-55099 Mainz, Germany

*To whom correspondence should be addressed. Tel: +49 6221 422349; Fax: +49 6221 422333; Email: hotz-wagenblatt{at}dkfz.de

In high throughput sequence analysis, it is often necessary to combine the results of contemporary bioinformatics tools, because no individual tool alone computes all the requested information. ESTAnnotator is a tool for the high throughput annotation of expressed sequence tags (ESTs) by automatically running a collection of bioinformatics applications. In the first step, a quality check is performed and repeats, vector parts and low quality sequences are masked. Then successive steps of database searching and EST clustering are performed. Already known transcripts present within mRNA and genomic DNA reference databases are identified. Subsequently, tools for the clustering of anonymous ESTs, and for further database searches at the protein level, are applied. Finally, the outputs of each individual tool are gathered and the relevant results presented in a descriptive summary. ESTAnnotator was already successfully applied for the systematic identification and characterisation of novel human genes involved in cartilage/bone formation, growth, differentiation and homeostasis. ESTAnnotator is available at http://genome.dkfz-heidelberg.de, contact: genome{at}dkfz.de.


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