potential orthologs as they were annotated as genes in later releases of Ensembl (51 and 52). In particular new human genes were annotated in these later releases at the same position where the pipeline described in this paper had placed the corresponding bovine gene. Intronic Sixteen cow sequences aligned completely within introns of annotated human genes. Of these sequences, 81% showed an overlap with existing genscan or ESTs features aligned in the same region of the human genome. Overall 19% of the results showed unreliable alignments. Not Aligned Among the bovine sequences that did not align to the human genome, 273 were protein coding, most (79%) were annotated as "novel genes" by Ensembl (Table (Table2). 2 ). When aligned with BLASTX against the protein non-redundant database at NCBI, 11% had a hit with human sequences, BAC clones and synthetic constructs (e.g. plasmids, clones) and 23% had a match with an E-value lower than 1e-10 with sequences from other species, such as sheep and goat. In addition, 29% showed similarity to the nucleotide database, both with human and bovine sequences, while the remaining 37% had no match at all. The problem of finding a significant match within this library is partly due to 25% of the sequences being less than 100 nucleotides in length, and therefore most are likely to be artefacts, short open reading frames or fragments of sequences, indeed 33% of them were located on unassigned chromosomes. Ensembl reported no evidence ( genscan models, ESTs, UniGene features) for 52%