I've been looking at the vignette for the annotationTools package and I had to send a message to the list to inform you of the incorrect use of the term "ortholog". The term "ortholog" is a special type/subset of "homolog", as too is "paralog". When talking about genes, these terms describe what we know about the evolutionary history of a gene. Homologous genes are related to each other by having the same common ancestor. Homologs can be further divided into orthologs and paralogs (among others which are more complex relations). Paralogs are those homologs that arise through gene duplication in a given species (past or present) while orthologs are genes related through speciation events. See here for a nice overview: http://en.wikipedia.org/wiki/Ortholog#Homology_of_sequences_in_genetic s Throughout the vignette, the term "ortholog" is used in error and should be changed to "homolog" - in all cases (without checking the context of every occurrence). HomoloGene provides links to homologous genes not orthologous genes. In fact, on their website they explicitly say: "Moreover, HomoloGene entries now include paralogs in addition to orthologs." Sorry to gripe, but it's an important distinction....people also mix up "homologous" and "similarity" when talking about the number of shared nucleotides or amino acids between two sequences. The former, says something about the evolutionary history/relationship of the genes whereas the other does not. Gripe over! Nath ------------------------------------------------------------- Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) OCE Post Doctoral Fellow CSIRO Livestock Industries J M Rendel Laboratory Rockhampton QLD 4701 Tel: +61 (0)7 4923 8121 Australia Fax: +61 (0)7 4923 8222 ------------------------------------------------------------- [[alternative HTML version deleted]]