genome. Forty sequences were known genes and three were novel genes (Table (Table2). 2 ). These sequences were translated in all six reading frames and BLASTed against the protein non-redundant database: for 35 a match was found with a bovine sequence and in the 29% of the cases the annotation and description corresponded to that for the human gene. Discussion Over the last decade, many different approaches for identifying gene orthology between species have been proposed in the literature. The process of gene annotation, as well as the discrimination between protein coding and non coding genes [ 39 ], will become even more important as the number of available genome sequences increases, in line with the rapid progress of the sequencing technology. Depending on the sensitivity and specificity of methods used to identify orthologous genes, the fraction of genes without orthologs between species is variable, and also depends on the quality of the genome assembly [ 40 , 41 ]. Among these genes, there are the so called orphans [ 32 ], which have no homologs among the genes of other species. Even though several explanations have been proposed for the absence of homologs, one of the possibilities is that they might represent species specific genes. In the literature, the search for orphans genes has been carried out in different species by comparing gene sets at protein level [ 34 , 42 , 43 ]. In the work presented here we faced the problem of non-orthologous genes between species at