Genome Research

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

Published online before print December 14, 2001, 10.1101/gr.200901
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
GR-2009Rv1
12/1/198    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Nekrutenko, A.
Right arrow Articles by Li, W.-H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Nekrutenko, A.
Right arrow Articles by Li, W.-H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 12, Issue 1, 198-202, January 2002

METHODS
The KA/KS Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study

Anton Nekrutenko, Kateryna D. Makova, and Wen-Hsiung Li1

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA

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.

1 Corresponding author.

12:198-202 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Genome Res.Home page
Y.-T. Huang, F.-C. Chen, C.-J. Chen, H.-L. Chen, and T.-J. Chuang
Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons
Genome Res., July 1, 2008; 18(7): 1163 - 1170.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
K. Van, D. H. Kim, C. M. Cai, M. Y. Kim, J. H. Shin, M. A. Graham, R. C. Shoemaker, B.-S. Choi, T.-J. Yang, and S.-H. Lee
Sequence Level Analysis of Recently Duplicated Regions in Soybean [Glycine max (L.) Merr.] Genome
DNA Res, April 1, 2008; 15(2): 93 - 102.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M.-S. Shiao, B.-Y. Liao, M. Long, and H.-T. Yu
Adaptive Evolution of the Insulin Two-Gene System in Mouse
Genetics, March 1, 2008; 178(3): 1683 - 1691.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
M. F. Lin, J. W. Carlson, M. A. Crosby, B. B. Matthews, C. Yu, S. Park, K. H. Wan, A. J. Schroeder, L. S. Gramates, S. E. St. Pierre, et al.
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
Genome Res., December 1, 2007; 17(12): 1823 - 1836.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
Z. E. Sauna, C. Kimchi-Sarfaty, S. V. Ambudkar, and M. M. Gottesman
Silent Polymorphisms Speak: How They Affect Pharmacogenomics and the Treatment of Cancer
Cancer Res., October 15, 2007; 67(20): 9609 - 9612.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
K. Hanada, X. Zhang, J. O. Borevitz, W.-H. Li, and S.-H. Shiu
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection
Genome Res., May 1, 2007; 17(5): 632 - 640.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
F. Biemar, D. A. Nix, J. Piel, B. Peterson, M. Ronshaugen, V. Sementchenko, I. Bell, J. R. Manak, and M. S. Levine
Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array
PNAS, August 22, 2006; 103(34): 12763 - 12768.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
I. Dupanloup and H. Kaessmann
Evolutionary simulations to detect functional lineage-specific genes
Bioinformatics, August 1, 2006; 22(15): 1815 - 1822.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
W. Wang, H. Zheng, C. Fan, J. Li, J. Shi, Z. Cai, G. Zhang, D. Liu, J. Zhang, S. Vang, et al.
High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes
PLANT CELL, August 1, 2006; 18(8): 1791 - 1802.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Liang, W. Zhou, and L. F. Landweber
SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W382 - W384.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
H. Yu, H. Jiang, Q. Zhou, J. Yang, Y. Cun, B. Su, C. Xiao, and W. Wang
Origination and evolution of a human-specific transmembrane protein gene, c1orf37-dup
Hum. Mol. Genet., June 1, 2006; 15(11): 1870 - 1875.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Xing and C. Lee
Assessing the application of Ka/Ks ratio test to alternatively spliced exons
Bioinformatics, October 1, 2005; 21(19): 3701 - 3703.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. L. Tupy, A. M. Bailey, G. Dailey, M. Evans-Holm, C. W. Siebel, S. Misra, S. E. Celniker, and G. M. Rubin
Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster
PNAS, April 12, 2005; 102(15): 5495 - 5500.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
S. Richards, Y. Liu, B. R. Bettencourt, P. Hradecky, S. Letovsky, R. Nielsen, K. Thornton, M. J. Hubisz, R. Chen, R. P. Meisel, et al.
Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
Genome Res., January 1, 2005; 15(1): 1 - 18.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Zheng, R. J. Roberts, and S. Kasif
Identification of genes with fast-evolving regions in microbial genomes
Nucleic Acids Res., December 2, 2004; 32(21): 6347 - 6357.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Ohtsuka, S. Horiuchi, J. K. Kulski, M. Kimura, and H. Inoko
CHOP: visualization of 'wobbling' and isolation of highly conserved regions from aligned DNA sequences
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W55 - W58.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Nekrutenko
Reconciling the Numbers: ESTs Versus Protein-Coding Genes
Mol. Biol. Evol., July 1, 2004; 21(7): 1278 - 1282.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Nekrutenko, W.-Y. Chung, and W.-H. Li
ETOPE: evolutionary test of predicted exons
Nucleic Acids Res., July 1, 2003; 31(13): 3564 - 3567.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. A. Thomas, B. Weston, M. Joseph, W. Wu, A. Nekrutenko, and P. J. Tonellato
Evolutionary Dynamics of Oncogenes and Tumor Suppressor Genes: Higher Intensities of Purifying Selection than Other Genes
Mol. Biol. Evol., June 1, 2003; 20(6): 964 - 968.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. Guigo, E. T. Dermitzakis, P. Agarwal, C. P. Ponting, G. Parra, A. Reymond, J. F. Abril, E. Keibler, R. Lyle, C. Ucla, et al.
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
PNAS, February 4, 2003; 100(3): 1140 - 1145.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.