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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.



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