RT Journal
A1 Birney, Ewan
A1 Clamp, Michele
A1 Durbin, Richard
T1 GeneWise and Genomewise
JF Genome Research 
JO Genome Research 
YR 2004 
FD May 01 
VO 14 
IS 5 
SP 988 
OP 995 
DO 10.1101/gr.1865504 
UL http://genome.cshlp.org/content/14/5/988.abstract 
AB 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.