The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
The KA/KS Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study
Open accessAbstract
Comparative genomics is a simple, powerful way to increase the accuracy of gene prediction. In this study, we show the utility of a simple test for the identification of protein-coding exons using human/mouse sequence comparisons. The test takes advantage of the fact that in the vast majority of coding regions, synonymous substitutions (KS) occur much more frequently than nonsynonymous ones (KA) and uses the KA/KS ratio as the criterion. We show the following: (1) most of the human and mouse exons are sufficiently long and have a suitable degree of sequence divergence for the test to perform reliably; (2) the test is suited for the identification of long exons and single exon genes, which are difficult to predict by current methods; (3) the test has a false-negative rate, lower than most of current gene prediction methods and a false-positive rate lower than all current methods; (4) the test has been automated and can be used in combination with other existing gene-prediction methods.
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Cites
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
Cited by
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
Stark, A., Lin, M. F., Kheradpour, P., Pedersen, J. S., Parts, L., Carlson, J. W., Crosby, M. A., Rasmussen, M. D., Roy, S., Deoras, A. N., et al. (2007) · Nature · doi:10.1038/nature06340 · Cited by 631
Richards, S., Liu, Y., Bettencourt, B. R., Hradecky, P., Letovsky, S., Nielsen, R., Thornton, K., Hubisz, M. J., Chen, R., Meisel, R. P., et al. (2005) · Genome Research · doi:10.1101/gr.3059305 · Cited by 498
Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames
Magny, E. G., Pueyo, J. I., Pearl, F. M. G., Cespedes, M. A., Niven, J. E., Bishop, S. A., & Couso, J. P. (2013) · Science · doi:10.1126/science.1238802 · Cited by 366
Sequence Divergence, Functional Constraint, and Selection in Protein Evolution
Fay, J. C., & Wu, C.-I. (2003) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.4.020303.162528 · Cited by 294
Metadata
- Authors
- Nekrutenko, A., Makova, K. D., & Li, W.-H.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2001-12-14
- Volume
- 12
- Issue
- 1
- Pages
- 198-202
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2152873040
- Cited by
- 324
- References
- 2
- Type
- posted content
- Language
- en
- Open access
- bronze
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