We have studied five methods of protein classification and have applie
d them to the 768 groups of related proteins in the PROSITE catalog. F
our of these methods are based on searching a database of blocks, and
the other uses the frequently occurring moths found in the protein fam
ilies combined with a fingerprint technique, Our experimental results
show that the block-based methods perform well when taking into accoun
t the probability of amino acids occurring in a block, Furthermore, th
e five methods give information that is complementary to each other, T
hus, using the five methods together, one can obtain high confidence c
lassifications (if the results agree) or suggest alternative hypothese
s (if the results disagree), We also list those proteins whose current
families documented in the PROSITE catalog differ from those suggeste
d by our results, There are remarkably few of them, which is a testimo
ny to the quality of PROSITE.