Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene.
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.
BioSciences Institute, University College Cork, Cork, Ireland. a.firth@ucc.ie
Andrew E
AE
Firth
John F
JF
Atkins
D000595:Amino Acid Sequence; D019295:Computational Biology; D017124:Conserved Sequence; D005807:Genes, Overlapping; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D020815:Polyproteins / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics; D019193:Waikavirus / Q000235:genetics*
D020815:Polyproteins; D012367:RNA, Viral; D014764:Viral Proteins