GeneWise and Genomewise
Ewan Birney, Michèle Clamp, Richard Durbin
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.
Topics & Concepts
EnsemblBiologyParsingHidden Markov modelComputational biologyAnnotationGeneGene predictionGene AnnotationGeneticsArtificial intelligenceBioinformaticsComputer scienceGenomicsGenomeGenomics and Phylogenetic StudiesRNA and protein synthesis mechanismsMachine Learning in Bioinformatics