The methods described to compensate for the incomplete annotation cov­erage of Chlamydomonas reinhardtii genes resulted in the addition of a vast number of unique annotations to the genome. While there is a strong overlap between pre-existing annotations and those assigned by inference, many new terms have also been added. The annotations derived by orthology,

however, are not mixed with the annotations attained directly to decrease the possibility of false positive associations of functional terms that may distort the analysis, and to permit a comparison with the functional terms derived directly from the Chlamydomonas annotation.