This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
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 arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Brocchieri, L.
Right arrow Articles by Mocarski, E. S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Brocchieri, L.
Right arrow Articles by Mocarski, E. S.

 Previous Article  |  Next Article 

Journal of Virology, June 2005, p. 7570-7596, Vol. 79, No. 12
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.12.7570-7596.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Predicting Coding Potential from Genome Sequence: Application to Betaherpesviruses Infecting Rats and Mice{dagger}

Luciano Brocchieri,1* Thomas N. Kledal,2,{ddagger} Samuel Karlin,1 and Edward S. Mocarski2*

Department of Mathematics,1 Department of Microbiology & Immunology, Stanford University, Stanford, California 943052

Received 9 December 2004/ Accepted 25 February 2005

Prediction of protein-coding regions and other features of primary DNA sequence have greatly contributed to experimental biology. Significant challenges remain in genome annotation methods, including the identification of small or overlapping genes and the assessment of mRNA splicing or unconventional translation signals in expression. We have employed a combined analysis of compositional biases and conservation together with frame-specific G+C representation to reevaluate and annotate the genome sequences of mouse and rat cytomegaloviruses. Our analysis predicts that there are at least 34 protein-coding regions in these genomes that were not apparent in earlier annotation efforts. These include 17 single-exon genes, three new exons of previously identified genes, a newly identified four-exon gene for a lectin-like protein (in rat cytomegalovirus), and 10 probable frameshift extensions of previously annotated genes. This expanded set of candidate genes provides an additional basis for investigation in cytomegalovirus biology and pathogenesis.

* Corresponding author. Mailing address for Luciano Brocchieri: Department of Mathematics, Stanford University, Stanford, CA 94305-2125. Phone: (650) 723-2221. Fax: (650) 725-2040. E-mail: luciano{at}stanford.edu. Mailing address for Edward S. Mocarski: Department of Microbiology & Immunology, Fairchild Science Building, Stanford University School of Medicine, CA 94305-5124. Phone: (650) 723-6435. Fax: (650) 723-1606. E-mail: mocarski{at}stanford.edu.

{dagger} Supplemental material for this article may be found at http://jvi.asm.org/.

{ddagger} Present address: Clinical Research Unit #136, HS Hvidovre Hospital, 2650 Hvidovre, Denmark.

Journal of Virology, June 2005, p. 7570-7596, Vol. 79, No. 12
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.12.7570-7596.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Norris, K. L., Youle, R. J. (2008). Cytomegalovirus Proteins vMIA and m38.5 Link Mitochondrial Morphogenesis to Bcl-2 Family Proteins. J. Virol. 82: 6232-6243 [Abstract] [Full Text]  
  • Jurak, I., Schumacher, U., Simic, H., Voigt, S., Brune, W. (2008). Murine Cytomegalovirus m38.5 Protein Inhibits Bax-Mediated Cell Death. J. Virol. 82: 4812-4822 [Abstract] [Full Text]  
  • Ahasan, M. M., Sweet, C. (2007). Murine cytomegalovirus open reading frame m29.1 augments virus replication both in vitro and in vivo. J. Gen. Virol. 88: 2941-2951 [Abstract] [Full Text]  
  • Terhune, S., Torigoi, E., Moorman, N., Silva, M., Qian, Z., Shenk, T., Yu, D. (2007). Human Cytomegalovirus UL38 Protein Blocks Apoptosis. J. Virol. 81: 3109-3123 [Abstract] [Full Text]  
  • Corbett, A. J., Forbes, C. A., Moro, D., Scalzo, A. A. (2007). Extensive sequence variation exists among isolates of murine cytomegalovirus within members of the m02 family of genes. J. Gen. Virol. 88: 758-769 [Abstract] [Full Text]  
  • Child, S. J., Hanson, L. K., Brown, C. E., Janzen, D. M., Geballe, A. P. (2006). Double-Stranded RNA Binding by a Heterodimeric Complex of Murine Cytomegalovirus m142 and m143 Proteins.. J. Virol. 80: 10173-10180 [Abstract] [Full Text]  
  • Tang, Q., Murphy, E. A., Maul, G. G. (2006). Experimental Confirmation of Global Murine Cytomegalovirus Open Reading Frames by Transcriptional Detection and Partial Characterization of Newly Described Gene Products. J. Virol. 80: 6873-6882 [Abstract] [Full Text]  
  • McCauley, S., Hein, J. (2006). Using hidden Markov models and observed evolution to annotate viral genomes. Bioinformatics 22: 1308-1316 [Abstract] [Full Text]  
  • Smith, G. B., Mocarski, E. S. (2005). Contribution of GADD45 Family Members to Cell Death Suppression by Cellular Bcl-xL and Cytomegalovirus vMIA. J. Virol. 79: 14923-14932 [Abstract] [Full Text]  
  • McCormick, A. L., Meiering, C. D., Smith, G. B., Mocarski, E. S. (2005). Mitochondrial Cell Death Suppressors Carried by Human and Murine Cytomegalovirus Confer Resistance to Proteasome Inhibitor-Induced Apoptosis. J. Virol. 79: 12205-12217 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»