With the parasite Neospora caninum contributing to great amounts of cattle deaths worldwide it has become an important target for control. N. caninum infected cattle appear symptom free until pregnancy, at which point the dormant N. caninum reverts to an actively dividing tachyzoite stage, the mechanism of this reactivation remains unknown. It is likely non-homologous or ‘orphan’ genes of N. caninum may be responsible. With no direct means to both store and search potentially involved genes with the flexibility required, both a website and MySQL database were created to support this investigation. The website, ApiBLAST (ApiBLAST.vetsci.co.uk), is an efficient tool to quickly locate, filter and analyse orphan genes. The database stores information on homology, derived from e-values determined by BLAST and subcellular localisation & structure determined by a number of tools maintained by the CBSA, including SignalP, TargetP and TMHMM. Twelve candidate genes were isolated from over 15,000, their functions not currently fully understood and thus possibly of interest for future investigation. ApiBLAST has great potential and flexibility as a bioinformatics tool, which this study has proven by the successful identification of the twelve candidate genes.