ENSEMBL Special

GeneWise and Genomewise

    • 1 The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    • 2 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Published May 3, 2004. Vol 14 Issue 5, pp. 988-995. https://doi.org/10.1101/gr.1865504
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cover of Genome Research Vol 36 Issue 4
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April 2026, Vol. 36, No. 4
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Abstract

We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure. Both algorithms are heavily used by the Ensembl annotation system. The GeneWise algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence.

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