Nucleic Acids Research, 2003, Vol. 31, No. 13 3564-3567
© 2003 Oxford University Press
ETOPE: evolutionary test of predicted exons
1 Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA 2 Center for Comparative Genomics and Bioinformatics, Penn State University, 108 Althouse Laboratory, University Park, PA 16802, USA 3 Department of Biochemistry and Molecular Biology, Penn State University, 108 Althouse Laboratory, University Park, PA 16802, USA 4 Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan 5 Center for Genomics Sciences, Academia Sinica, Taipei, 115 Taiwan
*To whom correspondence should be addressed at Department of Biochemistry and Molecular Biology, Penn State University, 108 Althouse Laboratory, University Park, PA 16802, USA. Tel: +1 814 863 1283; Fax: +1 814 863 7024; Email: aun1{at}psu.edu
Since a large number of computationally predicted exons are not supported by existing sequence (e.g. ESTs) or experimental (e.g. expression analysis) data they need to be validated by other methods. ETOPE is designed to test computational predictions by using signals that have not been included in any current computational prediction method. The test is based on the ratio of non-synonymous to synonymous substitution rates between sequences from different genomes. It has been previously shown, by empirical data and computer simulation, to be a powerful criterion for identifying protein-coding regions. The ETOPE is available at http://nekrut.uchicago.edu/etope/.
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