The work discussed herein was performed using the SAM HMM program suite on UltraSparc 140 workstations. SAM is programmed in ANSI C for Unix workstations. Information on obtaining SAM, as well as several World-Wide Web interfaces to SAM, can be found at http://www.cse.ucsc.edu/research/compbio/sam.html, or by sending email to sam-info@cse.ucsc.edu. The HMMer experiments were performed with HMMer version 1.8.1, while the SAM experiments used a pre-release of SAM version 2.0.