The matrix is not the whole set of parameterization for BLAST. There are also the gap costs and the lambda and K values used for computing E-values. Changing the matrix without correcting the other parameters leads to uninterpretable results. Kevin Karplus karplus at soe.ucsc.edu http://www.soe.ucsc.edu/~karplus Senior member, IEEE Board of Directors, ISCB (starting Jan 2005) Professor of Biomolecular Engineering, University of California, Santa Cruz Undergraduate and Graduate Director, Bioinformatics Affiliations for identification only.