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_genetics
 
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
 
 
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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
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