We study the performance of LP/DEE on a number of protein datasets with different characteristics (summarized in Table 1). The datasets are constructed from SwissProt [29], using the descriptions of [15] for the first two datasets, [36] for the next two, and [43] for the last one. These datasets are highly variable in the number and length of their protein sequences, as well as in the degree of motif conservation. The motif length parameters are set based on the lengths described by the above authors, and the BLOSUM62 substitution matrix is used for all reported results.