Using GeneWise in the Drosophila annotation experiment.
By Ewan Birney, Richard Durbin. Genome Research, 2000
415 citations recorded by the source corpus.
The GeneWise method for combining gene prediction and homology searches was applied to the 2.9-Mb region from Drosophila melanogaster. The results from the Genome Annotation Assessment Project (GASP) showed that GeneWise provided reasonably accurate gene predictions. Further investigation indicates that many of the incorrect gene predictions from GeneWise were due to transposons with valid protein-coding genes and the remaining cases are pseudogenes or possible annotation oversights.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/e04bfa687d7b0388a4acbbd3629c7588b236135e
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In Molecular Biology
- Steven L. Salzberg
- Richard Durbin
- C. Burge
- Heng Li
- Arek Kasprzyk
- Bernard Henrissat
- Brian J. Haas
- Arthur L. Delcher
Citations in the corpus
- Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma (2011, methodology): “Genes were predicted using Fgenesh [48], Fgenesh+ [49], and Genewise programs [50].”
- The Ensembl genome database project (2002, positive): “These positions are refined using genewise (7) to provide an accurate gene structure.”
- GeneWise and Genomewise. (2004, background): “It has also been assessed by a number of authors (Birney and Durbin 2000; Guigo et al. 2000; Yeh et al. 2001; Meyer and Durbin 2002).”
- Computational inference of homologous gene structures in the human genome. (2001, background): “A genomic region from human chromosome Xq28 containing seven annotated genes (Brenner et al. 1997) is illustrated in Figure 1B.”
- Automatic annotation of eukaryotic genes, pseudogenes and promoters (2006, methodology): “The program is very fast (Table 4), produces gene structures with similar accuracy to those of the relatively slow GeneWise program [16] and does not require knowledge of protein genomic location.”
- Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. (2003, methodology): “In addition, tools have been developed to incorporate EST alignments into gene predictions (14–16).”
- Alkylation damage in DNA and RNA--repair mechanisms and medical significance. (2004, methodology): “is identical to the sequence generated with the Genewise program[136] when theMacaca protein sequence (id BAB60797) is used to scan the human genome (F.”