Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning | Firth and Atkins Virology Journal 2010 7 17 http content 7 1 17 VIROLOGY JOURNAL RESEARCH Open Access Candidates in Astroviruses Seadornaviruses Cytorhabdoviruses and Coronaviruses for 1 frame overlapping genes accessed by leaky scanning Andrew E Firth 1 John F Atkins1 2 Abstract Background Overlapping genes are common in RNA viruses where they serve as a mechanism to optimize the coding potential of compact genomes. However annotation of overlapping genes can be difficult using conventional gene-finding software. Recently we have been using a number of complementary approaches to systematically identify previously undetected overlapping genes in RNA virus genomes. In this article we gather together a number of promising candidate new overlapping genes that may be of interest to the community. Results Overlapping gene predictions are presented for the astroviruses seadornaviruses cytorhabdoviruses and coronaviruses families Astroviridae Reoviridae Rhabdoviridae and Coronaviridae respectively . Background Overlapping genes whereby the same nucleotide sequence codes for two or more proteins in different reading frames are particularly c ommon in RNA viruses where they may serve as mechanisms to optimize the coding potential of compact genomes regulate gene expression or circumvent the host cell s canonical - though not ubiquitous - rule of one functional protein per mRNA . However such genes can be difficult to detect using conventional gene-finding software. MLOGD is a gene-finding program which was designed specifically for identifying overlapping coding sequences CDSs through the incorporation of explicit models for sequence evolution in multiply-coding regions 1-3 . One caveat is that de novo overlapping CDSs are often considerably less conserved than the ancestral genes that they overlap the ancestral gene is usually the known gene as it tends to be the longer of the two while the de novo gene is often very short . The explicit coding signal of
