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Parallel cascade recognition of exon and intron DNA sequences

Korenberg, M.J.; Lipson, E.D.; Green, J.R.; Solomon, J.E.

Annals of Biomedical Engineering 30(1): 129-140

2002


ISSN/ISBN: 0090-6964
PMID: 11874136
DOI: 10.1114/1.1433490
Accession: 011115732

Many of the current procedures for detecting coding regions on human DNA sequences combine a number of individual techniques such as discriminant analysis and neural net methods. Recent papers have used techniques from nonlinear systems identification, in particular, parallel cascade identification (PCI), as one means for classifying protein sequences into their structure/function groups. In the present paper, PCI is used in a pilot study to distinguish exon (coding) from intron (noncoding; interspersed within genes) human DNA sequences. Only the first exon and first intron sequences with known boundaries in genomic DNA from the beta T-cell receptor locus were used for training. Then, the parallel cascade classifiers were able to achieve classification rates of about 89% on novel sequences in a test set, and averaged about 82% when results of a blind test were included. In testing over a much wider range of human nucleotide sequences, PCI classifiers averaged 83.6% correct classifications. These results indicate that parallel cascade classifiers may be useful components in future coding region detection programs.

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