The Efficient Computation of Position- Specific Match Scores with the Fast Fourier Transform S. Rajasekaran 1 , X. Jin 1 , and J.L. Spouge 2 * * Corresponding Author 1 Department of Computer and Information Science and Engineering, University of Florida, Gainesville FL 32611 2 National Center for Biotechnology Information, National Library of Medicine, Bethesda MD 20894 Phone: (301) 435-5912 Fax: (301) 435-2433 Email: spouge@nih.gov For submission to the Journal of Computational Biology Running Title: PSSM Scores and the FFT Version Date: January 9, 2003