We would like to thank Saira Mian for many valuable suggestions, and David Haussler and the rest of the computational biology group at the Baskin Center for Computer Engineering and Information Sciences at UCSC for many suggestions and contributions. We also thank the anonymous referees for their excellent suggestions. This research was supported in part by NSF grants CDA-9115268 and BIR-9408579, a grant from CONNECT, Denmark, and a grant from the Novo-Nordisk Foundation. SAM source code, the experimental server, and SAM documentation can be accessed on the World-Wide Web at http://www.cse.ucsc.edu/research/compbio/sam.html or by sending electronic mail to sam-info@cse.ucsc.edu.