GeneWise and Genomewise (original) (raw)

1. Ewan Birney1,3,
2. Michele Clamp2, and
3. Richard Durbin2
4. 1 The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
5. 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.

• • Accepted January 13, 2004.
  • Received August 8, 2003.

• Cold Spring Harbor Laboratory Press

•