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GeneWise and Genomewise
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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The Ensembl annotation system predicts genes independently for each of its stages using GeneWise, in some cases in addition to previously predicted models using Genscan, and finally finds a consensus set of gene models.
“On the other hand, the Ensembl annotation system predicts genes independently for each of its “stages” (targeted, similarity, species-specific cDNA and EST, RNA-seq reads) using the gene prediction tool “GeneWise” (Birney et al. 2004), in some cases in addition to previously predicted models using “Genscan”. Finally, it finds a consensus set of gene models coming from all stages.”
From Annotation matters: the effect of structural gene annotation on orthology inference (2025) · cites this paper as Birney et al. 2004
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Metadata
- Authors
- Birney, E., Clamp, M., & Durbin, R.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2004-05
- Volume
- 14
- Issue
- 5
- Pages
- 988-995
- ISSN
- 1088-9051
- Cited by
- 2,542
- References
- 3
- Language
- en
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