Choice of Matrices Some matrices also incorporate additional information - STR matrix includes information about protein structure and can be used with very distantly related sequences Other matrices are specific for different types of proteins - SLIM (ScoreMatrix Leading to Intra-Membrane) and PHAT (Predicted Hydrophobic and Transmembrane matrix) are designed from/for membrane proteins (not soluble proteins) As of 2006, 94 matrices in GenomeNet 11:28 AM