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©Oxford University Press

A method for identifying splice sites and translational start sites in eukaryotic mRNA

Steven L. Salzberg

Department of Computer Science, 224 New Engineering Building. Johns Hopkins University Baltimore. MD 21218 USA E-mail: salzberg{at}cs.jhu.edu

This paper describes a new method for determining the consensus sequences that signal the start of translation and the boundaries between exons and introns (donor and acceptor sites) in eukaryotic mRNA. The method takes into account the dependencies between adjacent bases, in contrast to the usual technique of considering each position independently. When coupled with a dynamic program to compute the most likely sequence, new consensus sequences emerge. The consensus sequence information is summarized in conditional probability matrices which, when used to locate signals in uncharacterized genomic DNA, have greater sensitivity and specificity than conventional matrices. Species-specific versions of these matrices are especially effective at distinguishing true and false sites.

Received on October 21, 1996; accepted on February 12, 1997

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