GeneWise and Genomewise.

By Ewan Birney, Michele E. Clamp, Richard Durbin. Genome Research, 2004

2,550 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0863c14803246cf4cea42169c9fe0cfc94b03e6c

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Citations in the corpus

Genome sequence of the cultivated cotton Gossypium arboreum (2014, positive): “We next extracted target sequences from the genome, including a 2,000-bp extension at both ends of the alignment with intron regions, and again aligned the homologous protein sequences to these DNA fragments using GeneWise 49 (with parameters –trev –sum –genesf).”
A novel hybrid gene prediction method employing protein multiple sequence alignments (2011, background): “We also ran Genewise in HMM mode on the reference regions, with default parameters and supplied with a profileHMM in HMMER format, automatically generated from the same alignments, including the ex-ortholog ones.”
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. (2008, background): “Much attention has been given to developing alternative, extrinsic methods that use EST/cDNA to genome mapping, spliced alignments of known protein sequences, or patterns of conservation between related genomes (Gelfand et al. 1996; Mott 1997; Mathe et al. 2002; Birney et al. 2004; Stanke et al. 200”
Genome sequence and analysis of the tuber crop potato (2011, methodology): “vinifera and Oryza sativa ) onto the potato genome using TBLASTN with an E -value cut-off of 1 × 10 −5 , and then similar genome sequences were aligned against the matching proteins using Genewis”
The genome of the cucumber, Cucumis sativus L. (2009, methodology): “We aligned the protein sequences of five sequenced plants ( Arabidopsis , papaya, poplar, grapevine and rice) onto the cucumber genome using TBLASTN, at an E -value cutoff of 1 × 10 −5 , and the homologous genome sequences were aligned against the matching proteins using GeneWis”
Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family (2018, background): “© 2017 The Linnean Society of London, Zoological Journal of the Linnean Society, 2018, 182, 50–75 presented in Bleeker (1859). The first, Cephaloptera Olfeisii, equals C.”