The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Gene finding in novel genomes
Open accessAbstract
BACKGROUND: Computational gene prediction continues to be an important problem, especially for genomes with little experimental data. RESULTS: I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate. CONCLUSION: Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Cited by
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Stanke, M., Diekhans, M., Baertsch, R., & Haussler, D. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn013 · Cited by 2,605
BUSCO applications from quality assessments to gene prediction and phylogenomics
Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G., Kriventseva, E. V., & Zdobnov, E. M. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx319 · Cited by 2,214
Holt, C., & Yandell, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-491 · Cited by 2,118
Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium (2007) · Nature · doi:10.1038/nature06341 · Cited by 2,010
The genome of the cucumber,Cucumis sativus L
Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W. J., Wang, X., Xie, B., Ni, P., et al. (2009) · Nature Genetics · doi:10.1038/ng.475 · Cited by 1,490
Metadata
- Authors
- Korf, I.
- Venue
- BMC Bioinformatics
- Published
- 2004-05-14
- Volume
- 5
- Issue
- 1
- Pages
- 59-59
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W1484347389
- Cited by
- 3,192
- References
- 1
- FWCI
- 6.89
- Type
- journal article
- Language
- en
- Open access
- gold
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
