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Bioinformatics Vol. 19 no. 11 2003
Pages 1318-1324
© 2003 Oxford University Press

ESTprep: preprocessing cDNA sequence reads

Todd E. Scheetz 1,2,*, Nishank Trivedi 3, Chad A. Roberts 3, Tamara Kucaba 4, Brian Berger 4, Natalie L. Robinson 3, Clayton L. Birkett 3, Allen J. Gavin 3, Brian O’Leary 3, Terry A. Braun 1,3,5, Maria F. Bonaldo 4, John P. Robinson 3, Val C. Sheffield 4,8, Marcelo B. Soares 4,6,7 and Thomas L. Casavant 1,3,5

1 Center for Bioinformatics and Computational Biology
2 Department of Ophthalmology
3 Department of Electrical and Computer Engineering
4 Department of Pediatrics
5 Department of Biomedical Engineering
6 Department of Biochemistry
7 Department of Physiology
8 Howard Hughes Medical Institute, The University of Iowa, Iowa City, IA 52242, USA

Received on October 27, 2002 ; revised on November 3, 2002 ; accepted on February 6, 2003

Motivation: High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases.

Results: This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank.

Availability: The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html

Contact: tscheetz{at}eng.uiowa.edu

* To whom correspondence should be addressed.


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