GeneSplicer: a new computational method for splice site prediction - PubMed (original) (raw)

GeneSplicer: a new computational method for splice site prediction

M Pertea et al. Nucleic Acids Res. 2001.

Abstract

GeneSplicer is a new, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been tested successfully using DNA from two reference organisms: the model plant Arabidopsis thaliana and human. It was compared to six programs representing the leading splice site detectors for each of these species: NetPlantGene, NetGene2, HSPL, NNSplice, GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational efficiency.

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Figures

Figure 1

Figure 1

False positive versus false negative rates on human acceptor sites for GeneSplicer both with and without the local maximal score filter, and for NNSplice.

Figure 2

Figure 2

False positive versus false negative rates on human donor sites for GeneSplicer both with and without the local maximal score filter, and for NNSplice.

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References

    1. Burge C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78–94. - PubMed
    1. Brendel V. and Kleffe,J. (1998) Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. Nucleic Acids Res., 26, 4748–4757. - PMC - PubMed
    1. Berget S. (1995) Exon recognition in vertebrate splicing. J. Biol. Chem., 270, 2411–2414. - PubMed
    1. Moore M.J., Query,C.C. and Sharp,P.A. (1993) In Gesteland,R. and Atkins,J. (eds), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 303–357.
    1. Salzberg S., Delcher,A., Fasman,K. and Henderson,J. (1998) A decision tree system for finding genes in DNA. J. Comput. Biol., 5, 667–680. - PubMed

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