Perl pipeline for prediction of genes based on Guy Slater’s Exonerate. As used in Brown et al. Characterisation of retroviruses in the horse genome and their transcriptional activity via transcriptome sequencing. Virology in press 2012 and Tarlinton et al. Characterisation of a group of endogenous gammaretroviruses in the canine genome. The Veterinary Journal in press 2012