Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene.

John F Atkins, Andrew E Firth

Journal: Archives of virology 2008;153(7):1379-83

PMID: 18535758

Abstract

The genus Waikavirus belongs to the order Picornavirales, whose members all use a polyprotein expression strategy. With the exception of Theiler's virus, overlapping genes are essentially unknown in the order. Recently, we reported experimental verification for a new short overlapping coding sequence (CDS) in the Potyviridae-a family in which overlapping genes were previously unknown. Using the same bioinformatics software (MLOGD), we have identified an approximately 89-codon conserved open reading frame (ORF) with a strong coding signature in members of the genus Waikavirus. The ORF overlaps the polyprotein ORF but is in the +1 reading frame. Here, we describe the bioinformatic analysis.

Address: BioSciences Institute, University College Cork, Cork, Ireland. [email protected]

DOI: 10.1007/s00705-008-0119-5

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https://dx.doi.org/10.1007/s00705-008-0119-5

MeSH Terms: Amino Acid Sequence, Computational Biology, Conserved Sequence, Genes, Overlapping, Molecular Sequence Data, Open Reading Frames, Polyproteins, RNA, Viral, Sequence Alignment, Sequence Analysis, DNA, Viral Proteins, Waikavirus