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Genome Res. 14:988-995, 2004
©2004 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/04 $5.00
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ENSEMBL Special

GeneWise and Genomewise

Ewan Birney1,3, Michele Clamp2 and Richard Durbin2

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

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.

Footnotes

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1865504.

3 Corresponding author.
E-MAIL birney{at}ebi.ac.uk; FAX 44 1223 494468.


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