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© IRL Press Limited

Syntactic pattern analysis of 5'-splice site sequences of mRNA precursors in higher eukaryote genes

Mineichi Kudo *, YÔichi lida 1 and Masaru Shimbo

Division of Information Engineering, Graduate School of Engineering, Hokkaido University Sapporo 060, Japan
1Department of Chemistry, Faculty of Science, Hokkaido University Sapporo 060, Japan

* To whom reprint requests should be sent

The signals which direct the excision of introns from eukaryotic pre-mRNA are not yet well understood. In order to define the signals for 5'-splice sites of mRNA splicing, nucleotide sequences including 5'-splice junctions of mammalian pre-mRNAs are analysed by means of syntactic pattern analysis. Taking this approach, we infer the grammatical rules which specify 5'-splice sites and construct a finite automaton which is the recognizer of the nucleotide sequences at 5'-splice sites. By scanning the automaton along nucleotide sequences, we can identify the positions of 5'-splice junctions with a degree of discrimination of up to 94–97% in the known genes, while the degree of prediction is in the range 50–55% in new genes

Received on December 22, 1986; accepted on July 21, 1987

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