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Bioinformatics Vol. 17 no. 7 2001
Pages 602-607
© 2001 Oxford University Press

Identifying the 3'-terminal exon in human DNA

Jack E. Tabaska 1,2, Ramana V. Davuluri 1 and Michael Q. Zhang 1,*

1 Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA

Received on December 6, 2000 ; revised on January 30, 2001 ; accepted on February 2, 2001

Motivation: We present JTEF, a new program for finding 3' terminal exons in human DNA sequences. This program is based on quadratic discriminant analysis, a standard non-linear statistical pattern recognition method. The quadratic discriminant functions used for building the algorithm were trained on a set of 3' terminal exons of type 3tuexon (those containing the true STOP codon).

Results: We showed that the average predictive accuracy of JTEF is higher than the presently available best programs (GenScan and Genemark.hmm) based on a test set of 65 human DNA sequences with 121 genes. In particular JTEF performs well on larger genomic contigs containing multiple genes and significant amounts of intergenic DNA. It will become a valuable tool for genome annotation and gene functional studies.

Availability: JTEF is available free for academic users on request from ftp://cshl.org/pub/science/mzhanglab/JTEF and will be made available through the World Wide Web (http://argon.cshl.org/).

Contact: mzhang{at}cshl.org; ramana{at}cshl.org

* To whom correspondence should be addressed.

2 Present address: Monsanto Company, 800 North Lindbergh, St Louis, MO 63167, USA.


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