Correlation of length and quality of HMM descriptors. ATP-binding descriptors as well as face type descriptors for protein-protein interactions were run against original and shuffled versions of Swiss-Prot and uncharacterized NCBI sequences. We define the length of a profile Hidden Markov Model descriptor as its number of states. Quality is measured as difference between log E-values of best hit against original sequences and shuffled sequences. For Swiss-Prot, longer descriptors have better quality and therefore produce more significant hits. For uncharacterized sequences, this does not hold. One explanation could be that these sequences are depleted of significant matches by similarity searches.