% The regularizers are % blosum62 does Gribskov average score using the % Blosum-62 matrix (natural log base, 3 decimal places) % subst does matrix multiply with an optimized matrix % add_one adds 1 to each count % add_share adds 0.05 to each count % 1-comp adds pseudocounts, optimized for blocks database % 9-comp uses a 9-component Dirichlet mixture % 30-comp uses a 30-component Dirichlet mixture % For 0 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 0 Isoleucine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.074& 0.074& 0.085& 0.083\\ C & 0.025& 0.025& 0.019& 0.021\\ D & 0.054& 0.053& 0.049& 0.053\\ E & 0.054& 0.059& 0.057& 0.057\\ F & 0.047& 0.044& 0.039& 0.041\\ \hline G & 0.074& 0.079& 0.061& 0.076\\ H & 0.026& 0.026& 0.026& 0.025\\ \bf I &\bf 0.068&\bf 0.061&\bf 0.065&\bf 0.062\\ K & 0.058& 0.056& 0.058& 0.057\\ \bf L &\bf 0.099&\bf 0.085&\bf 0.085&\bf 0.090\\ \hline M & 0.025& 0.027& 0.031& 0.025\\ N & 0.045& 0.043& 0.046& 0.042\\ P & 0.039& 0.045& 0.033& 0.040\\ Q & 0.034& 0.037& 0.043& 0.037\\ R & 0.052& 0.051& 0.050& 0.051\\ \hline S & 0.057& 0.058& 0.072& 0.066\\ T & 0.051& 0.055& 0.061& 0.055\\ \bf V &\bf 0.073&\bf 0.070&\bf 0.077&\bf 0.074\\ W & 0.013& 0.016& 0.011& 0.013\\ Y & 0.032& 0.036& 0.031& 0.034\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is -0 bits % Probabilities for the components of 9-comp: % 0.1830 0.0576 0.0898 0.0793 0.0832 0.0911 0.1160 0.0660 0.2340 % encoding cost (-log2(probability(column)) with 9-comp is -0 bits % For 1 isoleucine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 1 Isoleucine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.046& 0.037\\ C & 0.018& 0.008& 0.010& 0.010\\ D & 0.020& 0.006& 0.026& 0.008\\ E & 0.020& 0.011& 0.031& 0.012\\ F & 0.044& 0.025& 0.021& 0.027\\ \hline G & 0.022& 0.011& 0.033& 0.012\\ H & 0.010& 0.005& 0.014& 0.006\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.495&\bf 0.472\\ K & 0.027& 0.011& 0.031& 0.014\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.046&\bf 0.117\\ \hline M & 0.037& 0.026& 0.017& 0.030\\ N & 0.017& 0.009& 0.025& 0.010\\ P & 0.018& 0.008& 0.018& 0.008\\ Q & 0.016& 0.008& 0.023& 0.010\\ R & 0.019& 0.010& 0.027& 0.012\\ \hline S & 0.027& 0.015& 0.039& 0.020\\ T & 0.048& 0.025& 0.033& 0.028\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.042&\bf 0.149\\ W & 0.006& 0.003& 0.006& 0.004\\ Y & 0.024& 0.011& 0.017& 0.013\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 3.93826 bits % Probabilities for the components of 9-comp: % 0.0566 0.0243 0.0318 0.0203 0.1936 0.4569 0.0159 0.1177 0.0830 % encoding cost (-log2(probability(column)) with 9-comp is 4.01438 bits % For 2 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 2 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.032& 0.025\\ C & 0.018& 0.008& 0.007& 0.007\\ D & 0.020& 0.006& 0.018& 0.005\\ E & 0.020& 0.011& 0.021& 0.007\\ F & 0.044& 0.025& 0.015& 0.018\\ \hline G & 0.022& 0.011& 0.023& 0.008\\ H & 0.010& 0.005& 0.010& 0.003\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.654&\bf 0.637\\ K & 0.027& 0.011& 0.021& 0.008\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.031&\bf 0.082\\ \hline M & 0.037& 0.026& 0.012& 0.020\\ N & 0.017& 0.009& 0.017& 0.006\\ P & 0.018& 0.008& 0.012& 0.005\\ Q & 0.016& 0.008& 0.016& 0.006\\ R & 0.019& 0.010& 0.018& 0.007\\ \hline S & 0.027& 0.015& 0.027& 0.012\\ T & 0.048& 0.025& 0.023& 0.018\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.028&\bf 0.117\\ W & 0.006& 0.003& 0.004& 0.002\\ Y & 0.024& 0.011& 0.012& 0.008\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 4.95219 bits % Probabilities for the components of 9-comp: % 0.0562 0.0226 0.0101 0.0144 0.1728 0.4870 0.0123 0.0645 0.1601 % encoding cost (-log2(probability(column)) with 9-comp is 5.09612 bits % For 3 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 3 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.024& 0.018\\ C & 0.018& 0.008& 0.005& 0.005\\ D & 0.020& 0.006& 0.014& 0.003\\ E & 0.020& 0.011& 0.016& 0.004\\ F & 0.044& 0.025& 0.011& 0.013\\ \hline G & 0.022& 0.011& 0.017& 0.006\\ H & 0.010& 0.005& 0.007& 0.002\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.737&\bf 0.737\\ K & 0.027& 0.011& 0.016& 0.005\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.024&\bf 0.059\\ \hline M & 0.037& 0.026& 0.009& 0.015\\ N & 0.017& 0.009& 0.013& 0.004\\ P & 0.018& 0.008& 0.009& 0.004\\ Q & 0.016& 0.008& 0.012& 0.004\\ R & 0.019& 0.010& 0.014& 0.004\\ \hline S & 0.027& 0.015& 0.020& 0.008\\ T & 0.048& 0.025& 0.017& 0.013\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.022&\bf 0.089\\ W & 0.006& 0.003& 0.003& 0.002\\ Y & 0.024& 0.011& 0.009& 0.006\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 5.56431 bits % Probabilities for the components of 9-comp: % 0.0560 0.0215 0.0039 0.0112 0.1528 0.4677 0.0103 0.0369 0.2396 % encoding cost (-log2(probability(column)) with 9-comp is 5.74567 bits % For 4 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 4 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.019& 0.013\\ C & 0.018& 0.008& 0.004& 0.004\\ D & 0.020& 0.006& 0.011& 0.003\\ E & 0.020& 0.011& 0.013& 0.003\\ F & 0.044& 0.025& 0.009& 0.009\\ \hline G & 0.022& 0.011& 0.014& 0.005\\ H & 0.010& 0.005& 0.006& 0.002\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.788&\bf 0.801\\ K & 0.027& 0.011& 0.013& 0.004\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.019&\bf 0.044\\ \hline M & 0.037& 0.026& 0.007& 0.011\\ N & 0.017& 0.009& 0.010& 0.003\\ P & 0.018& 0.008& 0.007& 0.003\\ Q & 0.016& 0.008& 0.010& 0.003\\ R & 0.019& 0.010& 0.011& 0.003\\ \hline S & 0.027& 0.015& 0.016& 0.006\\ T & 0.048& 0.025& 0.014& 0.010\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.017&\bf 0.069\\ W & 0.006& 0.003& 0.002& 0.001\\ Y & 0.024& 0.011& 0.007& 0.004\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 6.00443 bits % Probabilities for the components of 9-comp: % 0.0550 0.0203 0.0017 0.0091 0.1347 0.4330 0.0089 0.0223 0.3150 % encoding cost (-log2(probability(column)) with 9-comp is 6.1867 bits % For 5 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 5 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.016& 0.010\\ C & 0.018& 0.008& 0.004& 0.003\\ D & 0.020& 0.006& 0.009& 0.002\\ E & 0.020& 0.011& 0.011& 0.002\\ F & 0.044& 0.025& 0.008& 0.007\\ \hline G & 0.022& 0.011& 0.012& 0.004\\ H & 0.010& 0.005& 0.005& 0.001\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.822&\bf 0.846\\ K & 0.027& 0.011& 0.011& 0.003\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.016&\bf 0.034\\ \hline M & 0.037& 0.026& 0.006& 0.008\\ N & 0.017& 0.009& 0.009& 0.002\\ P & 0.018& 0.008& 0.006& 0.002\\ Q & 0.016& 0.008& 0.008& 0.002\\ R & 0.019& 0.010& 0.009& 0.002\\ \hline S & 0.027& 0.015& 0.014& 0.004\\ T & 0.048& 0.025& 0.012& 0.007\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.015&\bf 0.054\\ W & 0.006& 0.003& 0.002& 0.001\\ Y & 0.024& 0.011& 0.006& 0.003\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 6.34837 bits % Probabilities for the components of 9-comp: % 0.0533 0.0191 0.0008 0.0075 0.1188 0.3947 0.0077 0.0141 0.3839 % encoding cost (-log2(probability(column)) with 9-comp is 6.50652 bits % For 6 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 6 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.014& 0.008\\ C & 0.018& 0.008& 0.003& 0.002\\ D & 0.020& 0.006& 0.008& 0.002\\ E & 0.020& 0.011& 0.009& 0.002\\ F & 0.044& 0.025& 0.006& 0.006\\ \hline G & 0.022& 0.011& 0.010& 0.003\\ H & 0.010& 0.005& 0.004& 0.001\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.847&\bf 0.877\\ K & 0.027& 0.011& 0.009& 0.002\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.014&\bf 0.027\\ \hline M & 0.037& 0.026& 0.005& 0.006\\ N & 0.017& 0.009& 0.008& 0.002\\ P & 0.018& 0.008& 0.005& 0.002\\ Q & 0.016& 0.008& 0.007& 0.002\\ R & 0.019& 0.010& 0.008& 0.002\\ \hline S & 0.027& 0.015& 0.012& 0.004\\ T & 0.048& 0.025& 0.010& 0.006\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.013&\bf 0.043\\ W & 0.006& 0.003& 0.002& 0.001\\ Y & 0.024& 0.011& 0.005& 0.003\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 6.63073 bits % Probabilities for the components of 9-comp: % 0.0512 0.0179 0.0004 0.0063 0.1052 0.3576 0.0068 0.0093 0.4453 % encoding cost (-log2(probability(column)) with 9-comp is 6.74858 bits % For 7 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 7 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.012& 0.007\\ C & 0.018& 0.008& 0.003& 0.002\\ D & 0.020& 0.006& 0.007& 0.001\\ E & 0.020& 0.011& 0.008& 0.002\\ F & 0.044& 0.025& 0.006& 0.005\\ \hline G & 0.022& 0.011& 0.009& 0.003\\ H & 0.010& 0.005& 0.004& 0.001\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.866&\bf 0.901\\ K & 0.027& 0.011& 0.008& 0.002\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.012&\bf 0.021\\ \hline M & 0.037& 0.026& 0.004& 0.005\\ N & 0.017& 0.009& 0.007& 0.001\\ P & 0.018& 0.008& 0.005& 0.002\\ Q & 0.016& 0.008& 0.006& 0.001\\ R & 0.019& 0.010& 0.007& 0.002\\ \hline S & 0.027& 0.015& 0.010& 0.003\\ T & 0.048& 0.025& 0.009& 0.005\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.011&\bf 0.035\\ W & 0.006& 0.003& 0.002& 0.001\\ Y & 0.024& 0.011& 0.004& 0.002\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 6.87026 bits % Probabilities for the components of 9-comp: % 0.0490 0.0167 0.0002 0.0054 0.0935 0.3233 0.0060 0.0063 0.4995 % encoding cost (-log2(probability(column)) with 9-comp is 6.93758 bits % For 8 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 8 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.011& 0.006\\ C & 0.018& 0.008& 0.002& 0.002\\ D & 0.020& 0.006& 0.006& 0.001\\ E & 0.020& 0.011& 0.007& 0.001\\ F & 0.044& 0.025& 0.005& 0.004\\ \hline G & 0.022& 0.011& 0.008& 0.003\\ H & 0.010& 0.005& 0.003& 0.001\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.880&\bf 0.918\\ K & 0.027& 0.011& 0.007& 0.001\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.011&\bf 0.017\\ \hline M & 0.037& 0.026& 0.004& 0.004\\ N & 0.017& 0.009& 0.006& 0.001\\ P & 0.018& 0.008& 0.004& 0.002\\ Q & 0.016& 0.008& 0.006& 0.001\\ R & 0.019& 0.010& 0.006& 0.001\\ \hline S & 0.027& 0.015& 0.009& 0.002\\ T & 0.048& 0.025& 0.008& 0.004\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.010&\bf 0.028\\ W & 0.006& 0.003& 0.001& 0.001\\ Y & 0.024& 0.011& 0.004& 0.002\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 7.07826 bits % Probabilities for the components of 9-comp: % 0.0467 0.0156 0.0001 0.0046 0.0835 0.2926 0.0053 0.0044 0.5471 % encoding cost (-log2(probability(column)) with 9-comp is 7.08875 bits % For 9 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 9 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.010& 0.005\\ C & 0.018& 0.008& 0.002& 0.001\\ D & 0.020& 0.006& 0.006& 0.001\\ E & 0.020& 0.011& 0.007& 0.001\\ F & 0.044& 0.025& 0.005& 0.003\\ \hline G & 0.022& 0.011& 0.007& 0.002\\ H & 0.010& 0.005& 0.003& 0.001\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.892&\bf 0.932\\ K & 0.027& 0.011& 0.007& 0.001\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.010&\bf 0.014\\ \hline M & 0.037& 0.026& 0.004& 0.003\\ N & 0.017& 0.009& 0.005& 0.001\\ P & 0.018& 0.008& 0.004& 0.001\\ Q & 0.016& 0.008& 0.005& 0.001\\ R & 0.019& 0.010& 0.006& 0.001\\ \hline S & 0.027& 0.015& 0.008& 0.002\\ T & 0.048& 0.025& 0.007& 0.003\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.009&\bf 0.024\\ W & 0.006& 0.003& 0.001& 0.001\\ Y & 0.024& 0.011& 0.004& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 7.26208 bits % Probabilities for the components of 9-comp: % 0.0444 0.0146 0.0001 0.0040 0.0748 0.2653 0.0047 0.0032 0.5888 % encoding cost (-log2(probability(column)) with 9-comp is 7.21206 bits % For 10 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 10 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.009& 0.004\\ C & 0.018& 0.008& 0.002& 0.001\\ D & 0.020& 0.006& 0.005& 0.001\\ E & 0.020& 0.011& 0.006& 0.001\\ F & 0.044& 0.025& 0.004& 0.003\\ \hline G & 0.022& 0.011& 0.006& 0.002\\ H & 0.010& 0.005& 0.003& 0.001\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.902&\bf 0.942\\ K & 0.027& 0.011& 0.006& 0.001\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.009&\bf 0.012\\ \hline M & 0.037& 0.026& 0.003& 0.003\\ N & 0.017& 0.009& 0.005& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.005& 0.001\\ R & 0.019& 0.010& 0.005& 0.001\\ \hline S & 0.027& 0.015& 0.008& 0.002\\ T & 0.048& 0.025& 0.006& 0.003\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.008&\bf 0.020\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.003& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 7.42675 bits % Probabilities for the components of 9-comp: % 0.0423 0.0137 0.0001 0.0035 0.0674 0.2412 0.0043 0.0023 0.6253 % encoding cost (-log2(probability(column)) with 9-comp is 7.31431 bits % For 11 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 11 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.008& 0.003\\ C & 0.018& 0.008& 0.002& 0.001\\ D & 0.020& 0.006& 0.005& 0.001\\ E & 0.020& 0.011& 0.006& 0.001\\ F & 0.044& 0.025& 0.004& 0.002\\ \hline G & 0.022& 0.011& 0.006& 0.002\\ H & 0.010& 0.005& 0.003& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.910&\bf 0.951\\ K & 0.027& 0.011& 0.006& 0.001\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.008&\bf 0.010\\ \hline M & 0.037& 0.026& 0.003& 0.002\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.004& 0.001\\ R & 0.019& 0.010& 0.005& 0.001\\ \hline S & 0.027& 0.015& 0.007& 0.002\\ T & 0.048& 0.025& 0.006& 0.002\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.007&\bf 0.017\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.003& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 7.5759 bits % Probabilities for the components of 9-comp: % 0.0402 0.0129 0.0000 0.0031 0.0610 0.2199 0.0039 0.0017 0.6573 % encoding cost (-log2(probability(column)) with 9-comp is 7.4003 bits % For 12 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 12 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.008& 0.003\\ C & 0.018& 0.008& 0.002& 0.001\\ D & 0.020& 0.006& 0.004& 0.001\\ E & 0.020& 0.011& 0.005& 0.001\\ F & 0.044& 0.025& 0.004& 0.002\\ \hline G & 0.022& 0.011& 0.005& 0.002\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.917&\bf 0.957\\ K & 0.027& 0.011& 0.005& 0.001\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.008&\bf 0.008\\ \hline M & 0.037& 0.026& 0.003& 0.002\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.004& 0.001\\ R & 0.019& 0.010& 0.004& 0.001\\ \hline S & 0.027& 0.015& 0.006& 0.001\\ T & 0.048& 0.025& 0.005& 0.002\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.007&\bf 0.014\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.003& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 7.7122 bits % Probabilities for the components of 9-comp: % 0.0383 0.0121 0.0000 0.0028 0.0554 0.2011 0.0035 0.0013 0.6854 % encoding cost (-log2(probability(column)) with 9-comp is 7.47352 bits % For 13 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 13 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.007& 0.003\\ C & 0.018& 0.008& 0.002& 0.001\\ D & 0.020& 0.006& 0.004& 0.001\\ E & 0.020& 0.011& 0.005& 0.001\\ F & 0.044& 0.025& 0.003& 0.002\\ \hline G & 0.022& 0.011& 0.005& 0.002\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.923&\bf 0.963\\ K & 0.027& 0.011& 0.005& 0.001\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.007&\bf 0.007\\ \hline M & 0.037& 0.026& 0.003& 0.002\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.004& 0.001\\ R & 0.019& 0.010& 0.004& 0.001\\ \hline S & 0.027& 0.015& 0.006& 0.001\\ T & 0.048& 0.025& 0.005& 0.002\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.006&\bf 0.012\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.003& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 7.83769 bits % Probabilities for the components of 9-comp: % 0.0365 0.0114 0.0000 0.0025 0.0506 0.1846 0.0032 0.0010 0.7103 % encoding cost (-log2(probability(column)) with 9-comp is 7.53654 bits % For 14 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 14 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.007& 0.002\\ C & 0.018& 0.008& 0.001& 0.001\\ D & 0.020& 0.006& 0.004& 0.001\\ E & 0.020& 0.011& 0.004& 0.001\\ F & 0.044& 0.025& 0.003& 0.001\\ \hline G & 0.022& 0.011& 0.005& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.928&\bf 0.967\\ K & 0.027& 0.011& 0.004& 0.001\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.007&\bf 0.006\\ \hline M & 0.037& 0.026& 0.002& 0.002\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.003& 0.000\\ R & 0.019& 0.010& 0.004& 0.001\\ \hline S & 0.027& 0.015& 0.006& 0.001\\ T & 0.048& 0.025& 0.005& 0.002\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.006&\bf 0.011\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 7.95395 bits % Probabilities for the components of 9-comp: % 0.0348 0.0107 0.0000 0.0022 0.0463 0.1699 0.0029 0.0008 0.7323 % encoding cost (-log2(probability(column)) with 9-comp is 7.5913 bits % For 15 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 15 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.006& 0.002\\ C & 0.018& 0.008& 0.001& 0.001\\ D & 0.020& 0.006& 0.004& 0.001\\ E & 0.020& 0.011& 0.004& 0.001\\ F & 0.044& 0.025& 0.003& 0.001\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.932&\bf 0.971\\ K & 0.027& 0.011& 0.004& 0.001\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.006&\bf 0.005\\ \hline M & 0.037& 0.026& 0.002& 0.001\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.000\\ R & 0.019& 0.010& 0.004& 0.001\\ \hline S & 0.027& 0.015& 0.005& 0.001\\ T & 0.048& 0.025& 0.004& 0.001\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.006&\bf 0.009\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 8.06226 bits % Probabilities for the components of 9-comp: % 0.0332 0.0101 0.0000 0.0020 0.0426 0.1569 0.0027 0.0006 0.7518 % encoding cost (-log2(probability(column)) with 9-comp is 7.63931 bits % For 16 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 16 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.006& 0.002\\ C & 0.018& 0.008& 0.001& 0.001\\ D & 0.020& 0.006& 0.003& 0.001\\ E & 0.020& 0.011& 0.004& 0.001\\ F & 0.044& 0.025& 0.003& 0.001\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.936&\bf 0.974\\ K & 0.027& 0.011& 0.004& 0.001\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.006&\bf 0.005\\ \hline M & 0.037& 0.026& 0.002& 0.001\\ N & 0.017& 0.009& 0.003& 0.000\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.000\\ R & 0.019& 0.010& 0.003& 0.001\\ \hline S & 0.027& 0.015& 0.005& 0.001\\ T & 0.048& 0.025& 0.004& 0.001\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.005&\bf 0.008\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 8.16364 bits % Probabilities for the components of 9-comp: % 0.0318 0.0096 0.0000 0.0018 0.0393 0.1453 0.0025 0.0005 0.7693 % encoding cost (-log2(probability(column)) with 9-comp is 7.68171 bits % For 17 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 17 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.006& 0.002\\ C & 0.018& 0.008& 0.001& 0.001\\ D & 0.020& 0.006& 0.003& 0.000\\ E & 0.020& 0.011& 0.004& 0.001\\ F & 0.044& 0.025& 0.003& 0.001\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.940&\bf 0.977\\ K & 0.027& 0.011& 0.004& 0.000\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.005&\bf 0.004\\ \hline M & 0.037& 0.026& 0.002& 0.001\\ N & 0.017& 0.009& 0.003& 0.000\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.000\\ R & 0.019& 0.010& 0.003& 0.001\\ \hline S & 0.027& 0.015& 0.005& 0.001\\ T & 0.048& 0.025& 0.004& 0.001\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.005&\bf 0.007\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 8.25891 bits % Probabilities for the components of 9-comp: % 0.0304 0.0091 0.0000 0.0016 0.0364 0.1349 0.0023 0.0004 0.7849 % encoding cost (-log2(probability(column)) with 9-comp is 7.71943 bits % For 18 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 18 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.005& 0.001\\ C & 0.018& 0.008& 0.001& 0.000\\ D & 0.020& 0.006& 0.003& 0.000\\ E & 0.020& 0.011& 0.004& 0.000\\ F & 0.044& 0.025& 0.002& 0.001\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.943&\bf 0.979\\ K & 0.027& 0.011& 0.004& 0.000\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.005&\bf 0.004\\ \hline M & 0.037& 0.026& 0.002& 0.001\\ N & 0.017& 0.009& 0.003& 0.000\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.000\\ R & 0.019& 0.010& 0.003& 0.000\\ \hline S & 0.027& 0.015& 0.004& 0.001\\ T & 0.048& 0.025& 0.004& 0.001\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.005&\bf 0.006\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.000\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 8.34877 bits % Probabilities for the components of 9-comp: % 0.0292 0.0086 0.0000 0.0015 0.0338 0.1256 0.0021 0.0003 0.7989 % encoding cost (-log2(probability(column)) with 9-comp is 7.75321 bits % For 19 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 19 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.005& 0.001\\ C & 0.018& 0.008& 0.001& 0.000\\ D & 0.020& 0.006& 0.003& 0.000\\ E & 0.020& 0.011& 0.003& 0.000\\ F & 0.044& 0.025& 0.002& 0.001\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.946&\bf 0.981\\ K & 0.027& 0.011& 0.003& 0.000\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.005&\bf 0.003\\ \hline M & 0.037& 0.026& 0.002& 0.001\\ N & 0.017& 0.009& 0.003& 0.000\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.000\\ R & 0.019& 0.010& 0.003& 0.000\\ \hline S & 0.027& 0.015& 0.004& 0.001\\ T & 0.048& 0.025& 0.004& 0.001\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.004&\bf 0.006\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.000\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 8.4338 bits % Probabilities for the components of 9-comp: % 0.0280 0.0082 0.0000 0.0014 0.0314 0.1172 0.0020 0.0003 0.8115 % encoding cost (-log2(probability(column)) with 9-comp is 7.78362 bits % For 20 isoleucines, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 20 Isoleucines} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.055& 0.028& 0.005& 0.001\\ C & 0.018& 0.008& 0.001& 0.000\\ D & 0.020& 0.006& 0.003& 0.000\\ E & 0.020& 0.011& 0.003& 0.000\\ F & 0.044& 0.025& 0.002& 0.001\\ \hline G & 0.022& 0.011& 0.003& 0.001\\ H & 0.010& 0.005& 0.001& 0.000\\ \bf I &\bf 0.253&\bf 0.517&\bf 0.948&\bf 0.983\\ K & 0.027& 0.011& 0.003& 0.000\\ \bf L &\bf 0.147&\bf 0.117&\bf 0.005&\bf 0.003\\ \hline M & 0.037& 0.026& 0.002& 0.001\\ N & 0.017& 0.009& 0.003& 0.000\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.002& 0.000\\ R & 0.019& 0.010& 0.003& 0.000\\ \hline S & 0.027& 0.015& 0.004& 0.001\\ T & 0.048& 0.025& 0.003& 0.001\\ \bf V &\bf 0.171&\bf 0.146&\bf 0.004&\bf 0.005\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.000\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 8.5145 bits % Probabilities for the components of 9-comp: % 0.0269 0.0078 0.0000 0.0013 0.0293 0.1097 0.0018 0.0002 0.8229 % encoding cost (-log2(probability(column)) with 9-comp is 7.81116 bits ClassName = DirichletReg Name = posterior_20I Alphabet = ExtAA Order = A C D E F G H I K L M N P Q R S T V W Y AlphaChar= 20 NumDistr= 9 Number= 0 Mixture= 0.0268902 Alpha= 21.1806 0.270671 0.039848 0.017576 0.016415 0.014268 0.131916 0.012391 20.0226 0.020358 0.030727 0.015315 0.048298 0.053803 0.020662 0.023612 0.216147 0.147226 0.065438 0.003758 0.009621 Comment= S , A T , N G P C , Q R K H D , E Y >< M W I F V , L Number= 1 Mixture= 0.00784407 Alpha= 21.3558 0.021465 0.0103 0.011741 0.010883 0.385651 0.016416 0.076196 20.0353 0.013921 0.093517 0.022034 0.028593 0.013086 0.023011 0.018866 0.029156 0.018153 0.0361 0.07177 0.419641 Comment= Y , F W , H ,, N Q S R , K L M D E C P T >< I A G , V Number= 2 Mixture= 1.70334e-06 Alpha= 26.6644 0.561459 0.045448 0.438366 0.764167 0.087364 0.259114 0.21494 20.1459 0.762204 0.24732 0.118662 0.441564 0.174822 0.53084 0.465529 0.583402 0.445586 0.22705 0.02951 0.12109 Comment= K Q E , N R D S H , T A , P Y G , M W F C , L , V >< I Number= 3 Mixture= 0.00126709 Alpha= 22.0814 0.070143 0.01114 0.019479 0.094657 0.013162 0.048038 0.077 20.0329 0.576639 0.072293 0.02824 0.080372 0.037661 0.185037 0.506783 0.073732 0.071587 0.042532 0.011254 0.028723 Comment= K , R , Q , H N E , S , T Y P W A G D , M C L >< I F , V Number= 4 Mixture= 0.0293113 Alpha= 22.081 0.041103 0.014794 0.00561 0.010216 0.153602 0.007797 0.007175 20.2996 0.010849 0.999446 0.210189 0.006127 0.013021 0.019798 0.014509 0.012049 0.035799 0.180085 0.012744 0.026466 Comment= L M F ,, Q W Y , T V C R A H K E P >< S I N D , G Number= 5 Mixture= 0.109661 Alpha= 22.5682 0.115607 0.037381 0.012414 0.018179 0.051778 0.017255 0.004911 20.7969 0.017074 0.285858 0.075811 0.014548 0.015092 0.011382 0.012696 0.027535 0.088333 0.94434 0.004373 0.016741 Comment= V , T M A L , C F S K , E N Y Q D R P W >< I H G Number= 6 Mixture= 0.00184814 Alpha= 21.7661 0.093461 0.004737 0.387252 0.347841 0.010822 0.105877 0.049776 20.015 0.094276 0.027761 0.01004 0.187869 0.050018 0.110039 0.038668 0.119471 0.065802 0.02543 0.003215 0.018742 Comment= D E , N Q , K H S , G P R , T A Y ,>< I W F M C , L , V Number= 7 Mixture= 0.000227901 Alpha= 24.9877 0.452171 0.114613 0.06246 0.115702 0.284246 0.140204 0.100358 20.5502 0.143995 0.700649 0.27658 0.118569 0.09747 0.126673 0.143634 0.278983 0.358482 0.66175 0.061533 0.199373 Comment= Y S Q T H , K A M F N R W E C L , P D G V ,,>< I Number= 8 Mixture= 0.822948 Alpha= 20.0995 0.005193 0.004039 0.006722 0.006121 0.003468 0.016931 0.003647 20.0022 0.005019 0.00599 0.001473 0.004158 0.009055 0.00363 0.006583 0.003172 0.00369 0.002967 0.002772 0.002686 Comment= I >< G P D R H W E K Q N , C Y S , F T A , M L ,, V EndClassName = DirichletReg % For 0 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 0 Isoleucine, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.033& 0.013& 0.046& 0.020\\ C & 0.014& 0.005& 0.010& 0.006\\ D & 0.015& 0.007& 0.026& 0.010\\ E & 0.024& 0.009& 0.031& 0.012\\ F & 0.053& 0.041& 0.021& 0.047\\ \hline G & 0.033& 0.012& 0.033& 0.016\\ H & 0.012& 0.007& 0.014& 0.013\\ \bf I &\bf 0.030&\bf 0.013&\bf 0.035&\bf 0.019\\ K & 0.026& 0.010& 0.031& 0.016\\ \bf L &\bf 0.070&\bf 0.033&\bf 0.046&\bf 0.037\\ \hline M & 0.018& 0.008& 0.017& 0.010\\ N & 0.013& 0.009& 0.025& 0.011\\ P & 0.011& 0.006& 0.018& 0.009\\ Q & 0.019& 0.009& 0.023& 0.011\\ R & 0.023& 0.013& 0.027& 0.015\\ \hline S & 0.026& 0.011& 0.039& 0.016\\ T & 0.023& 0.009& 0.033& 0.014\\ \bf V &\bf 0.033&\bf 0.015&\bf 0.042&\bf 0.021\\ W & 0.465& 0.729& 0.466& 0.649\\ Y & 0.058& 0.041& 0.017& 0.048\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 6.55725 bits % Probabilities for the components of 9-comp: % 0.0460 0.2407 0.0314 0.0338 0.0402 0.0122 0.0167 0.0643 0.5146 % encoding cost (-log2(probability(column)) with 9-comp is 6.30268 bits % For 1 isoleucine and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 1 Isoleucine, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.060& 0.025& 0.032& 0.032\\ C & 0.022& 0.007& 0.007& 0.008\\ D & 0.024& 0.006& 0.018& 0.007\\ E & 0.031& 0.010& 0.021& 0.011\\ F & 0.068& 0.029& 0.015& 0.045\\ \hline G & 0.038& 0.011& 0.023& 0.011\\ H & 0.015& 0.005& 0.010& 0.011\\ \bf I &\bf 0.122&\bf 0.412&\bf 0.339&\bf 0.298\\ K & 0.037& 0.011& 0.021& 0.014\\ \bf L &\bf 0.141&\bf 0.100&\bf 0.031&\bf 0.099\\ \hline M & 0.036& 0.022& 0.012& 0.028\\ N & 0.020& 0.009& 0.017& 0.011\\ P & 0.020& 0.008& 0.012& 0.008\\ Q & 0.025& 0.008& 0.016& 0.012\\ R & 0.029& 0.011& 0.018& 0.013\\ \hline S & 0.037& 0.014& 0.027& 0.020\\ T & 0.046& 0.022& 0.023& 0.025\\ \bf V &\bf 0.104&\bf 0.118&\bf 0.028&\bf 0.073\\ W & 0.074& 0.155& 0.319& 0.238\\ Y & 0.052& 0.017& 0.012& 0.036\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 11.3844 bits % Probabilities for the components of 9-comp: % 0.0255 0.1929 0.0319 0.0193 0.2090 0.1462 0.0048 0.3158 0.0546 % encoding cost (-log2(probability(column)) with 9-comp is 12.0424 bits % For 2 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 2 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.061& 0.026& 0.024& 0.023\\ C & 0.022& 0.008& 0.005& 0.006\\ D & 0.024& 0.006& 0.014& 0.004\\ E & 0.028& 0.010& 0.016& 0.007\\ F & 0.061& 0.027& 0.011& 0.035\\ \hline G & 0.033& 0.011& 0.017& 0.008\\ H & 0.013& 0.005& 0.007& 0.008\\ \bf I &\bf 0.162&\bf 0.459&\bf 0.497&\bf 0.447\\ K & 0.035& 0.011& 0.016& 0.009\\ \bf L &\bf 0.149&\bf 0.107&\bf 0.024&\bf 0.080\\ \hline M & 0.038& 0.024& 0.009& 0.021\\ N & 0.020& 0.009& 0.013& 0.007\\ P & 0.020& 0.008& 0.009& 0.006\\ Q & 0.022& 0.008& 0.012& 0.008\\ R & 0.027& 0.010& 0.014& 0.009\\ \hline S & 0.034& 0.015& 0.020& 0.014\\ T & 0.048& 0.023& 0.017& 0.018\\ \bf V &\bf 0.128&\bf 0.130&\bf 0.022&\bf 0.063\\ W & 0.034& 0.088& 0.243& 0.200\\ Y & 0.042& 0.015& 0.009& 0.027\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 12.9443 bits % Probabilities for the components of 9-comp: % 0.0274 0.1995 0.0142 0.0164 0.2231 0.1927 0.0044 0.2349 0.0874 % encoding cost (-log2(probability(column)) with 9-comp is 13.7876 bits % For 3 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 3 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.060& 0.027& 0.019& 0.017\\ C & 0.021& 0.008& 0.004& 0.005\\ D & 0.023& 0.006& 0.011& 0.003\\ E & 0.026& 0.010& 0.013& 0.005\\ F & 0.057& 0.027& 0.009& 0.028\\ \hline G & 0.030& 0.011& 0.014& 0.006\\ H & 0.013& 0.005& 0.006& 0.006\\ \bf I &\bf 0.184&\bf 0.477&\bf 0.595&\bf 0.553\\ K & 0.033& 0.011& 0.013& 0.006\\ \bf L &\bf 0.150&\bf 0.110&\bf 0.019&\bf 0.064\\ \hline M & 0.038& 0.025& 0.007& 0.017\\ N & 0.019& 0.009& 0.010& 0.005\\ P & 0.020& 0.008& 0.007& 0.004\\ Q & 0.021& 0.008& 0.010& 0.005\\ R & 0.025& 0.010& 0.011& 0.006\\ \hline S & 0.033& 0.015& 0.016& 0.010\\ T & 0.049& 0.024& 0.014& 0.013\\ \bf V &\bf 0.140&\bf 0.135&\bf 0.017&\bf 0.052\\ W & 0.022& 0.062& 0.196& 0.173\\ Y & 0.037& 0.014& 0.007& 0.022\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 13.9515 bits % Probabilities for the components of 9-comp: % 0.0297 0.2084 0.0070 0.0147 0.2257 0.2164 0.0041 0.1677 0.1262 % encoding cost (-log2(probability(column)) with 9-comp is 14.9483 bits % For 4 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 4 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.059& 0.027& 0.016& 0.013\\ C & 0.021& 0.008& 0.004& 0.004\\ D & 0.022& 0.006& 0.009& 0.002\\ E & 0.025& 0.010& 0.011& 0.004\\ F & 0.055& 0.026& 0.008& 0.023\\ \hline G & 0.028& 0.011& 0.012& 0.004\\ H & 0.012& 0.005& 0.005& 0.005\\ \bf I &\bf 0.197&\bf 0.486&\bf 0.660&\bf 0.631\\ K & 0.032& 0.011& 0.011& 0.005\\ \bf L &\bf 0.151&\bf 0.112&\bf 0.016&\bf 0.052\\ \hline M & 0.038& 0.025& 0.006& 0.013\\ N & 0.019& 0.009& 0.009& 0.004\\ P & 0.019& 0.008& 0.006& 0.003\\ Q & 0.020& 0.008& 0.008& 0.004\\ R & 0.024& 0.010& 0.009& 0.005\\ \hline S & 0.032& 0.015& 0.014& 0.007\\ T & 0.049& 0.024& 0.012& 0.010\\ \bf V &\bf 0.146&\bf 0.138&\bf 0.015&\bf 0.044\\ W & 0.017& 0.048& 0.164& 0.151\\ Y & 0.034& 0.013& 0.006& 0.018\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 14.7015 bits % Probabilities for the components of 9-comp: % 0.0313 0.2135 0.0037 0.0132 0.2214 0.2262 0.0039 0.1197 0.1671 % encoding cost (-log2(probability(column)) with 9-comp is 15.8023 bits % For 5 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 5 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.059& 0.027& 0.014& 0.010\\ C & 0.020& 0.008& 0.003& 0.003\\ D & 0.022& 0.006& 0.008& 0.002\\ E & 0.024& 0.010& 0.009& 0.003\\ F & 0.053& 0.026& 0.006& 0.019\\ \hline G & 0.027& 0.011& 0.010& 0.004\\ H & 0.012& 0.005& 0.004& 0.004\\ \bf I &\bf 0.206&\bf 0.492&\bf 0.708&\bf 0.688\\ K & 0.031& 0.011& 0.009& 0.004\\ \bf L &\bf 0.150&\bf 0.113&\bf 0.014&\bf 0.043\\ \hline M & 0.038& 0.025& 0.005& 0.011\\ N & 0.018& 0.009& 0.008& 0.003\\ P & 0.019& 0.008& 0.005& 0.003\\ Q & 0.019& 0.008& 0.007& 0.003\\ R & 0.023& 0.010& 0.008& 0.004\\ \hline S & 0.031& 0.015& 0.012& 0.005\\ T & 0.049& 0.025& 0.010& 0.008\\ \bf V &\bf 0.151&\bf 0.139&\bf 0.013&\bf 0.037\\ W & 0.015& 0.039& 0.141& 0.134\\ Y & 0.032& 0.013& 0.005& 0.015\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 15.3003 bits % Probabilities for the components of 9-comp: % 0.0323 0.2150 0.0021 0.0119 0.2132 0.2273 0.0037 0.0865 0.2080 % encoding cost (-log2(probability(column)) with 9-comp is 16.4676 bits % For 6 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 6 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.058& 0.027& 0.012& 0.008\\ C & 0.020& 0.008& 0.003& 0.002\\ D & 0.022& 0.006& 0.007& 0.002\\ E & 0.024& 0.010& 0.008& 0.002\\ F & 0.052& 0.026& 0.006& 0.016\\ \hline G & 0.026& 0.011& 0.009& 0.003\\ H & 0.011& 0.005& 0.004& 0.003\\ \bf I &\bf 0.213&\bf 0.496&\bf 0.743&\bf 0.733\\ K & 0.031& 0.011& 0.008& 0.003\\ \bf L &\bf 0.150&\bf 0.114&\bf 0.012&\bf 0.036\\ \hline M & 0.038& 0.025& 0.004& 0.009\\ N & 0.018& 0.009& 0.007& 0.002\\ P & 0.019& 0.008& 0.005& 0.002\\ Q & 0.019& 0.008& 0.006& 0.002\\ R & 0.022& 0.010& 0.007& 0.003\\ \hline S & 0.030& 0.015& 0.010& 0.004\\ T & 0.049& 0.025& 0.009& 0.006\\ \bf V &\bf 0.154&\bf 0.140&\bf 0.011&\bf 0.031\\ W & 0.013& 0.034& 0.124& 0.120\\ Y & 0.031& 0.012& 0.004& 0.013\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 15.7993 bits % Probabilities for the components of 9-comp: % 0.0328 0.2138 0.0012 0.0108 0.2031 0.2235 0.0034 0.0635 0.2478 % encoding cost (-log2(probability(column)) with 9-comp is 17.0065 bits % For 7 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 7 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.058& 0.027& 0.011& 0.007\\ C & 0.020& 0.008& 0.002& 0.002\\ D & 0.022& 0.006& 0.006& 0.001\\ E & 0.023& 0.010& 0.007& 0.002\\ F & 0.051& 0.026& 0.005& 0.014\\ \hline G & 0.026& 0.011& 0.008& 0.003\\ H & 0.011& 0.005& 0.003& 0.003\\ \bf I &\bf 0.217&\bf 0.499&\bf 0.771&\bf 0.767\\ K & 0.030& 0.011& 0.007& 0.002\\ \bf L &\bf 0.150&\bf 0.114&\bf 0.011&\bf 0.030\\ \hline M & 0.038& 0.026& 0.004& 0.007\\ N & 0.018& 0.009& 0.006& 0.002\\ P & 0.019& 0.008& 0.004& 0.002\\ Q & 0.018& 0.008& 0.006& 0.002\\ R & 0.022& 0.010& 0.006& 0.002\\ \hline S & 0.030& 0.015& 0.009& 0.003\\ T & 0.049& 0.025& 0.008& 0.005\\ \bf V &\bf 0.156&\bf 0.141&\bf 0.010&\bf 0.026\\ W & 0.012& 0.029& 0.110& 0.108\\ Y & 0.030& 0.012& 0.004& 0.011\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 16.227 bits % Probabilities for the components of 9-comp: % 0.0330 0.2108 0.0008 0.0098 0.1924 0.2167 0.0032 0.0473 0.2860 % encoding cost (-log2(probability(column)) with 9-comp is 17.4556 bits % For 8 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 8 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.058& 0.027& 0.010& 0.006\\ C & 0.020& 0.008& 0.002& 0.002\\ D & 0.021& 0.006& 0.006& 0.001\\ E & 0.023& 0.010& 0.007& 0.001\\ F & 0.050& 0.026& 0.005& 0.012\\ \hline G & 0.025& 0.011& 0.007& 0.002\\ H & 0.011& 0.005& 0.003& 0.002\\ \bf I &\bf 0.221&\bf 0.501&\bf 0.794&\bf 0.795\\ K & 0.030& 0.011& 0.007& 0.002\\ \bf L &\bf 0.150&\bf 0.115&\bf 0.010&\bf 0.026\\ \hline M & 0.038& 0.026& 0.004& 0.006\\ N & 0.018& 0.009& 0.005& 0.002\\ P & 0.019& 0.008& 0.004& 0.002\\ Q & 0.018& 0.008& 0.005& 0.002\\ R & 0.022& 0.010& 0.006& 0.002\\ \hline S & 0.030& 0.015& 0.008& 0.003\\ T & 0.049& 0.025& 0.007& 0.004\\ \bf V &\bf 0.158&\bf 0.141&\bf 0.009&\bf 0.023\\ W & 0.011& 0.026& 0.100& 0.099\\ Y & 0.029& 0.012& 0.004& 0.010\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 16.6016 bits % Probabilities for the components of 9-comp: % 0.0329 0.2066 0.0005 0.0089 0.1816 0.2084 0.0030 0.0359 0.3223 % encoding cost (-log2(probability(column)) with 9-comp is 17.8378 bits % For 9 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 9 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.058& 0.027& 0.009& 0.005\\ C & 0.020& 0.008& 0.002& 0.001\\ D & 0.021& 0.006& 0.005& 0.001\\ E & 0.023& 0.010& 0.006& 0.001\\ F & 0.050& 0.026& 0.004& 0.011\\ \hline G & 0.025& 0.011& 0.006& 0.002\\ H & 0.011& 0.005& 0.003& 0.002\\ \bf I &\bf 0.224&\bf 0.503&\bf 0.812&\bf 0.818\\ K & 0.030& 0.011& 0.006& 0.002\\ \bf L &\bf 0.149&\bf 0.115&\bf 0.009&\bf 0.022\\ \hline M & 0.038& 0.026& 0.003& 0.005\\ N & 0.018& 0.009& 0.005& 0.001\\ P & 0.019& 0.008& 0.003& 0.001\\ Q & 0.018& 0.008& 0.005& 0.001\\ R & 0.021& 0.010& 0.005& 0.002\\ \hline S & 0.029& 0.015& 0.008& 0.002\\ T & 0.049& 0.025& 0.006& 0.004\\ \bf V &\bf 0.159&\bf 0.142&\bf 0.008&\bf 0.020\\ W & 0.010& 0.024& 0.091& 0.091\\ Y & 0.029& 0.012& 0.003& 0.009\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 16.9346 bits % Probabilities for the components of 9-comp: % 0.0326 0.2017 0.0003 0.0081 0.1711 0.1993 0.0028 0.0276 0.3565 % encoding cost (-log2(probability(column)) with 9-comp is 18.1689 bits % For 10 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 10 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.027& 0.008& 0.004\\ C & 0.019& 0.008& 0.002& 0.001\\ D & 0.021& 0.006& 0.005& 0.001\\ E & 0.022& 0.010& 0.006& 0.001\\ F & 0.049& 0.026& 0.004& 0.009\\ \hline G & 0.025& 0.011& 0.006& 0.002\\ H & 0.011& 0.005& 0.003& 0.002\\ \bf I &\bf 0.227&\bf 0.504&\bf 0.828&\bf 0.836\\ K & 0.030& 0.011& 0.006& 0.001\\ \bf L &\bf 0.149&\bf 0.115&\bf 0.008&\bf 0.019\\ \hline M & 0.038& 0.026& 0.003& 0.004\\ N & 0.018& 0.009& 0.004& 0.001\\ P & 0.019& 0.008& 0.003& 0.001\\ Q & 0.018& 0.008& 0.004& 0.001\\ R & 0.021& 0.010& 0.005& 0.001\\ \hline S & 0.029& 0.015& 0.007& 0.002\\ T & 0.048& 0.025& 0.006& 0.003\\ \bf V &\bf 0.160&\bf 0.142&\bf 0.007&\bf 0.017\\ W & 0.010& 0.022& 0.083& 0.084\\ Y & 0.028& 0.012& 0.003& 0.008\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 17.2346 bits % Probabilities for the components of 9-comp: % 0.0322 0.1963 0.0002 0.0074 0.1611 0.1900 0.0026 0.0215 0.3887 % encoding cost (-log2(probability(column)) with 9-comp is 18.4594 bits % For 11 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 11 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.027& 0.008& 0.004\\ C & 0.019& 0.008& 0.002& 0.001\\ D & 0.021& 0.006& 0.004& 0.001\\ E & 0.022& 0.010& 0.005& 0.001\\ F & 0.049& 0.026& 0.004& 0.008\\ \hline G & 0.025& 0.011& 0.005& 0.002\\ H & 0.011& 0.005& 0.002& 0.002\\ \bf I &\bf 0.229&\bf 0.506&\bf 0.841&\bf 0.852\\ K & 0.029& 0.011& 0.005& 0.001\\ \bf L &\bf 0.149&\bf 0.115&\bf 0.008&\bf 0.017\\ \hline M & 0.038& 0.026& 0.003& 0.004\\ N & 0.018& 0.009& 0.004& 0.001\\ P & 0.019& 0.008& 0.003& 0.001\\ Q & 0.018& 0.008& 0.004& 0.001\\ R & 0.021& 0.010& 0.004& 0.001\\ \hline S & 0.029& 0.015& 0.006& 0.002\\ T & 0.048& 0.025& 0.005& 0.003\\ \bf V &\bf 0.161&\bf 0.143&\bf 0.007&\bf 0.015\\ W & 0.009& 0.020& 0.077& 0.078\\ Y & 0.028& 0.012& 0.003& 0.007\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 17.5074 bits % Probabilities for the components of 9-comp: % 0.0317 0.1906 0.0001 0.0068 0.1517 0.1808 0.0025 0.0170 0.4188 % encoding cost (-log2(probability(column)) with 9-comp is 18.7174 bits % For 12 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 12 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.027& 0.007& 0.003\\ C & 0.019& 0.008& 0.002& 0.001\\ D & 0.021& 0.006& 0.004& 0.001\\ E & 0.022& 0.010& 0.005& 0.001\\ F & 0.048& 0.026& 0.003& 0.007\\ \hline G & 0.024& 0.011& 0.005& 0.001\\ H & 0.011& 0.005& 0.002& 0.001\\ \bf I &\bf 0.231&\bf 0.507&\bf 0.852&\bf 0.865\\ K & 0.029& 0.011& 0.005& 0.001\\ \bf L &\bf 0.149&\bf 0.115&\bf 0.007&\bf 0.015\\ \hline M & 0.038& 0.026& 0.003& 0.003\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.019& 0.008& 0.003& 0.001\\ Q & 0.018& 0.008& 0.004& 0.001\\ R & 0.021& 0.010& 0.004& 0.001\\ \hline S & 0.029& 0.015& 0.006& 0.002\\ T & 0.048& 0.025& 0.005& 0.002\\ \bf V &\bf 0.162&\bf 0.143&\bf 0.006&\bf 0.013\\ W & 0.009& 0.019& 0.071& 0.072\\ Y & 0.028& 0.012& 0.003& 0.006\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 17.7576 bits % Probabilities for the components of 9-comp: % 0.0311 0.1849 0.0001 0.0063 0.1429 0.1719 0.0023 0.0135 0.4471 % encoding cost (-log2(probability(column)) with 9-comp is 18.9487 bits % For 13 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 13 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.028& 0.007& 0.003\\ C & 0.019& 0.008& 0.001& 0.001\\ D & 0.021& 0.006& 0.004& 0.001\\ E & 0.022& 0.010& 0.004& 0.001\\ F & 0.048& 0.026& 0.003& 0.007\\ \hline G & 0.024& 0.011& 0.005& 0.001\\ H & 0.011& 0.005& 0.002& 0.001\\ \bf I &\bf 0.233&\bf 0.507&\bf 0.862&\bf 0.877\\ K & 0.029& 0.011& 0.004& 0.001\\ \bf L &\bf 0.149&\bf 0.116&\bf 0.007&\bf 0.013\\ \hline M & 0.038& 0.026& 0.002& 0.003\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.019& 0.008& 0.003& 0.001\\ Q & 0.017& 0.008& 0.003& 0.001\\ R & 0.021& 0.010& 0.004& 0.001\\ \hline S & 0.029& 0.015& 0.006& 0.001\\ T & 0.048& 0.025& 0.005& 0.002\\ \bf V &\bf 0.163&\bf 0.143&\bf 0.006&\bf 0.012\\ W & 0.009& 0.018& 0.067& 0.068\\ Y & 0.027& 0.012& 0.002& 0.006\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 17.9886 bits % Probabilities for the components of 9-comp: % 0.0305 0.1791 0.0001 0.0058 0.1347 0.1633 0.0022 0.0109 0.4734 % encoding cost (-log2(probability(column)) with 9-comp is 19.1577 bits % For 14 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 14 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.028& 0.006& 0.002\\ C & 0.019& 0.008& 0.001& 0.001\\ D & 0.021& 0.006& 0.004& 0.001\\ E & 0.022& 0.010& 0.004& 0.001\\ F & 0.048& 0.026& 0.003& 0.006\\ \hline G & 0.024& 0.011& 0.004& 0.001\\ H & 0.011& 0.005& 0.002& 0.001\\ \bf I &\bf 0.234&\bf 0.508&\bf 0.870&\bf 0.886\\ K & 0.029& 0.011& 0.004& 0.001\\ \bf L &\bf 0.149&\bf 0.116&\bf 0.006&\bf 0.012\\ \hline M & 0.038& 0.026& 0.002& 0.003\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.019& 0.008& 0.002& 0.001\\ Q & 0.017& 0.008& 0.003& 0.001\\ R & 0.021& 0.010& 0.004& 0.001\\ \hline S & 0.028& 0.015& 0.005& 0.001\\ T & 0.048& 0.025& 0.004& 0.002\\ \bf V &\bf 0.163&\bf 0.143&\bf 0.006&\bf 0.011\\ W & 0.009& 0.017& 0.063& 0.064\\ Y & 0.027& 0.012& 0.002& 0.005\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 18.2032 bits % Probabilities for the components of 9-comp: % 0.0298 0.1735 0.0001 0.0053 0.1271 0.1552 0.0021 0.0089 0.4981 % encoding cost (-log2(probability(column)) with 9-comp is 19.3478 bits % For 15 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 15 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.028& 0.006& 0.002\\ C & 0.019& 0.008& 0.001& 0.001\\ D & 0.021& 0.006& 0.003& 0.001\\ E & 0.022& 0.010& 0.004& 0.001\\ F & 0.048& 0.026& 0.003& 0.005\\ \hline G & 0.024& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.001\\ \bf I &\bf 0.235&\bf 0.509&\bf 0.878&\bf 0.895\\ K & 0.029& 0.011& 0.004& 0.001\\ \bf L &\bf 0.149&\bf 0.116&\bf 0.006&\bf 0.010\\ \hline M & 0.038& 0.026& 0.002& 0.002\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.019& 0.008& 0.002& 0.001\\ Q & 0.017& 0.008& 0.003& 0.001\\ R & 0.021& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.005& 0.001\\ T & 0.048& 0.025& 0.004& 0.002\\ \bf V &\bf 0.164&\bf 0.143&\bf 0.005&\bf 0.009\\ W & 0.008& 0.016& 0.059& 0.060\\ Y & 0.027& 0.012& 0.002& 0.005\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 18.4036 bits % Probabilities for the components of 9-comp: % 0.0292 0.1680 0.0000 0.0050 0.1200 0.1474 0.0019 0.0073 0.5212 % encoding cost (-log2(probability(column)) with 9-comp is 19.5219 bits % For 16 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 16 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.028& 0.006& 0.002\\ C & 0.019& 0.008& 0.001& 0.001\\ D & 0.021& 0.006& 0.003& 0.001\\ E & 0.022& 0.010& 0.004& 0.001\\ F & 0.047& 0.026& 0.003& 0.005\\ \hline G & 0.024& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.001\\ \bf I &\bf 0.236&\bf 0.509&\bf 0.885&\bf 0.902\\ K & 0.029& 0.011& 0.004& 0.001\\ \bf L &\bf 0.148&\bf 0.116&\bf 0.005&\bf 0.009\\ \hline M & 0.038& 0.026& 0.002& 0.002\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.019& 0.008& 0.002& 0.001\\ Q & 0.017& 0.008& 0.003& 0.001\\ R & 0.021& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.005& 0.001\\ T & 0.048& 0.025& 0.004& 0.001\\ \bf V &\bf 0.164&\bf 0.144&\bf 0.005&\bf 0.009\\ W & 0.008& 0.015& 0.056& 0.057\\ Y & 0.027& 0.012& 0.002& 0.004\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 18.5915 bits % Probabilities for the components of 9-comp: % 0.0285 0.1626 0.0000 0.0046 0.1135 0.1402 0.0018 0.0060 0.5427 % encoding cost (-log2(probability(column)) with 9-comp is 19.6822 bits % For 17 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 17 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.028& 0.005& 0.002\\ C & 0.019& 0.008& 0.001& 0.001\\ D & 0.021& 0.006& 0.003& 0.000\\ E & 0.022& 0.010& 0.004& 0.001\\ F & 0.047& 0.026& 0.002& 0.004\\ \hline G & 0.024& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.001\\ \bf I &\bf 0.237&\bf 0.510&\bf 0.891&\bf 0.909\\ K & 0.029& 0.011& 0.004& 0.001\\ \bf L &\bf 0.148&\bf 0.116&\bf 0.005&\bf 0.008\\ \hline M & 0.037& 0.026& 0.002& 0.002\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.019& 0.008& 0.002& 0.001\\ Q & 0.017& 0.008& 0.003& 0.001\\ R & 0.020& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.004& 0.001\\ T & 0.048& 0.025& 0.004& 0.001\\ \bf V &\bf 0.165&\bf 0.144&\bf 0.005&\bf 0.008\\ W & 0.008& 0.014& 0.053& 0.054\\ Y & 0.027& 0.012& 0.002& 0.004\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 18.7684 bits % Probabilities for the components of 9-comp: % 0.0278 0.1574 0.0000 0.0043 0.1074 0.1333 0.0017 0.0050 0.5629 % encoding cost (-log2(probability(column)) with 9-comp is 19.8305 bits % For 18 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 18 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.028& 0.005& 0.002\\ C & 0.019& 0.008& 0.001& 0.001\\ D & 0.021& 0.006& 0.003& 0.000\\ E & 0.021& 0.010& 0.003& 0.001\\ F & 0.047& 0.026& 0.002& 0.004\\ \hline G & 0.024& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.001\\ \bf I &\bf 0.238&\bf 0.510&\bf 0.896&\bf 0.915\\ K & 0.029& 0.011& 0.003& 0.001\\ \bf L &\bf 0.148&\bf 0.116&\bf 0.005&\bf 0.008\\ \hline M & 0.037& 0.026& 0.002& 0.002\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.017& 0.008& 0.003& 0.001\\ R & 0.020& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.004& 0.001\\ T & 0.048& 0.025& 0.004& 0.001\\ \bf V &\bf 0.165&\bf 0.144&\bf 0.004&\bf 0.007\\ W & 0.008& 0.014& 0.050& 0.051\\ Y & 0.026& 0.012& 0.002& 0.004\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 18.9356 bits % Probabilities for the components of 9-comp: % 0.0272 0.1525 0.0000 0.0040 0.1018 0.1269 0.0016 0.0042 0.5817 % encoding cost (-log2(probability(column)) with 9-comp is 19.9682 bits % For 19 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 19 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.028& 0.005& 0.002\\ C & 0.019& 0.008& 0.001& 0.001\\ D & 0.021& 0.006& 0.003& 0.000\\ E & 0.021& 0.010& 0.003& 0.000\\ F & 0.047& 0.025& 0.002& 0.004\\ \hline G & 0.023& 0.011& 0.003& 0.001\\ H & 0.010& 0.005& 0.001& 0.001\\ \bf I &\bf 0.239&\bf 0.510&\bf 0.901&\bf 0.920\\ K & 0.029& 0.011& 0.003& 0.001\\ \bf L &\bf 0.148&\bf 0.116&\bf 0.005&\bf 0.007\\ \hline M & 0.037& 0.026& 0.002& 0.002\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.017& 0.008& 0.002& 0.000\\ R & 0.020& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.004& 0.001\\ T & 0.048& 0.025& 0.003& 0.001\\ \bf V &\bf 0.165&\bf 0.144&\bf 0.004&\bf 0.006\\ W & 0.008& 0.013& 0.048& 0.049\\ Y & 0.026& 0.012& 0.002& 0.003\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 19.094 bits % Probabilities for the components of 9-comp: % 0.0265 0.1477 0.0000 0.0037 0.0966 0.1209 0.0016 0.0036 0.5994 % encoding cost (-log2(probability(column)) with 9-comp is 20.0967 bits % For 20 isoleucines and one tryptophan, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 20 Isoleucines, 1 Tryptophan} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.028& 0.005& 0.001\\ C & 0.019& 0.008& 0.001& 0.000\\ D & 0.021& 0.006& 0.003& 0.000\\ E & 0.021& 0.010& 0.003& 0.000\\ F & 0.047& 0.025& 0.002& 0.003\\ \hline G & 0.023& 0.011& 0.003& 0.001\\ H & 0.010& 0.005& 0.001& 0.001\\ \bf I &\bf 0.239&\bf 0.511&\bf 0.905&\bf 0.925\\ K & 0.028& 0.011& 0.003& 0.000\\ \bf L &\bf 0.148&\bf 0.116&\bf 0.004&\bf 0.006\\ \hline M & 0.037& 0.026& 0.002& 0.001\\ N & 0.017& 0.009& 0.002& 0.000\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.017& 0.008& 0.002& 0.000\\ R & 0.020& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.004& 0.001\\ T & 0.048& 0.025& 0.003& 0.001\\ \bf V &\bf 0.166&\bf 0.144&\bf 0.004&\bf 0.006\\ W & 0.008& 0.013& 0.046& 0.047\\ Y & 0.026& 0.012& 0.002& 0.003\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 19.2445 bits % Probabilities for the components of 9-comp: % 0.0259 0.1431 0.0000 0.0035 0.0918 0.1153 0.0015 0.0030 0.6159 % encoding cost (-log2(probability(column)) with 9-comp is 20.217 bits % For 0 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 0 Isoleucine, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.067& 0.050& 0.046& 0.047\\ C & 0.022& 0.011& 0.010& 0.011\\ D & 0.019& 0.008& 0.026& 0.010\\ E & 0.025& 0.014& 0.031& 0.014\\ F & 0.043& 0.019& 0.021& 0.022\\ \hline G & 0.027& 0.015& 0.033& 0.018\\ H & 0.009& 0.005& 0.014& 0.007\\ \bf I &\bf 0.154&\bf 0.120&\bf 0.035&\bf 0.124\\ K & 0.033& 0.014& 0.031& 0.016\\ \bf L &\bf 0.113&\bf 0.078&\bf 0.046&\bf 0.086\\ \hline M & 0.028& 0.019& 0.017& 0.024\\ N & 0.020& 0.008& 0.025& 0.012\\ P & 0.017& 0.011& 0.018& 0.010\\ Q & 0.020& 0.009& 0.023& 0.011\\ R & 0.023& 0.011& 0.027& 0.013\\ \hline S & 0.041& 0.018& 0.039& 0.028\\ T & 0.046& 0.035& 0.033& 0.032\\ \bf V &\bf 0.262&\bf 0.541&\bf 0.502&\bf 0.498\\ W & 0.006& 0.003& 0.006& 0.004\\ Y & 0.023& 0.010& 0.017& 0.012\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 3.70068 bits % Probabilities for the components of 9-comp: % 0.1362 0.0206 0.0411 0.0218 0.0967 0.4499 0.0224 0.1177 0.0937 % encoding cost (-log2(probability(column)) with 9-comp is 3.74721 bits % For 1 isoleucine and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 1 Isoleucine, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.062& 0.039& 0.032& 0.028\\ C & 0.021& 0.010& 0.007& 0.009\\ D & 0.020& 0.007& 0.018& 0.004\\ E & 0.023& 0.012& 0.021& 0.006\\ F & 0.044& 0.022& 0.015& 0.016\\ \hline G & 0.025& 0.013& 0.023& 0.006\\ H & 0.010& 0.005& 0.010& 0.003\\ \bf I &\bf 0.200&\bf 0.314&\bf 0.339&\bf 0.370\\ K & 0.031& 0.013& 0.021& 0.006\\ \bf L &\bf 0.130&\bf 0.097&\bf 0.031&\bf 0.079\\ \hline M & 0.033& 0.022& 0.012& 0.021\\ N & 0.019& 0.009& 0.017& 0.005\\ P & 0.018& 0.009& 0.012& 0.005\\ Q & 0.018& 0.008& 0.016& 0.005\\ R & 0.022& 0.011& 0.018& 0.005\\ \hline S & 0.034& 0.017& 0.027& 0.010\\ T & 0.047& 0.030& 0.023& 0.022\\ \bf V &\bf 0.215&\bf 0.348&\bf 0.344&\bf 0.395\\ W & 0.006& 0.003& 0.004& 0.002\\ Y & 0.024& 0.011& 0.012& 0.006\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 8.52782 bits % Probabilities for the components of 9-comp: % 0.0114 0.0025 0.0063 0.0019 0.0760 0.8121 0.0010 0.0874 0.0015 % encoding cost (-log2(probability(column)) with 9-comp is 6.76185 bits % For 2 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 2 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.060& 0.035& 0.024& 0.022\\ C & 0.020& 0.009& 0.005& 0.007\\ D & 0.020& 0.007& 0.014& 0.003\\ E & 0.022& 0.012& 0.016& 0.004\\ F & 0.044& 0.023& 0.011& 0.012\\ \hline G & 0.024& 0.012& 0.017& 0.004\\ H & 0.010& 0.005& 0.007& 0.002\\ \bf I &\bf 0.217&\bf 0.381&\bf 0.497&\bf 0.489\\ K & 0.029& 0.012& 0.016& 0.004\\ \bf L &\bf 0.136&\bf 0.104&\bf 0.024&\bf 0.062\\ \hline M & 0.034& 0.024& 0.009& 0.016\\ N & 0.018& 0.009& 0.013& 0.003\\ P & 0.018& 0.009& 0.009& 0.003\\ Q & 0.017& 0.008& 0.012& 0.003\\ R & 0.021& 0.010& 0.014& 0.003\\ \hline S & 0.031& 0.016& 0.020& 0.007\\ T & 0.048& 0.029& 0.017& 0.017\\ \bf V &\bf 0.200&\bf 0.281&\bf 0.261&\bf 0.332\\ W & 0.006& 0.003& 0.003& 0.001\\ Y & 0.024& 0.011& 0.009& 0.005\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 10.0877 bits % Probabilities for the components of 9-comp: % 0.0099 0.0021 0.0023 0.0013 0.0654 0.8639 0.0007 0.0524 0.0019 % encoding cost (-log2(probability(column)) with 9-comp is 8.1973 bits % For 3 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 3 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.059& 0.034& 0.019& 0.018\\ C & 0.019& 0.009& 0.004& 0.006\\ D & 0.020& 0.007& 0.011& 0.002\\ E & 0.021& 0.011& 0.013& 0.003\\ F & 0.044& 0.024& 0.009& 0.010\\ \hline G & 0.023& 0.012& 0.014& 0.003\\ H & 0.010& 0.005& 0.006& 0.001\\ \bf I &\bf 0.226&\bf 0.415&\bf 0.595&\bf 0.570\\ K & 0.029& 0.012& 0.013& 0.003\\ \bf L &\bf 0.139&\bf 0.107&\bf 0.019&\bf 0.051\\ \hline M & 0.035& 0.024& 0.007& 0.013\\ N & 0.018& 0.009& 0.010& 0.003\\ P & 0.018& 0.009& 0.007& 0.003\\ Q & 0.017& 0.008& 0.010& 0.002\\ R & 0.020& 0.010& 0.011& 0.003\\ \hline S & 0.030& 0.016& 0.016& 0.005\\ T & 0.048& 0.028& 0.014& 0.014\\ \bf V &\bf 0.193&\bf 0.248&\bf 0.211&\bf 0.284\\ W & 0.006& 0.003& 0.002& 0.001\\ Y & 0.024& 0.011& 0.007& 0.003\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 11.0949 bits % Probabilities for the components of 9-comp: % 0.0098 0.0020 0.0010 0.0011 0.0606 0.8881 0.0006 0.0343 0.0026 % encoding cost (-log2(probability(column)) with 9-comp is 9.23043 bits % For 4 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 4 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.058& 0.032& 0.016& 0.016\\ C & 0.019& 0.009& 0.004& 0.005\\ D & 0.020& 0.007& 0.009& 0.002\\ E & 0.021& 0.011& 0.011& 0.003\\ F & 0.044& 0.024& 0.008& 0.008\\ \hline G & 0.023& 0.012& 0.012& 0.003\\ H & 0.010& 0.005& 0.005& 0.001\\ \bf I &\bf 0.231&\bf 0.435&\bf 0.660&\bf 0.628\\ K & 0.029& 0.012& 0.011& 0.003\\ \bf L &\bf 0.140&\bf 0.109&\bf 0.016&\bf 0.044\\ \hline M & 0.035& 0.025& 0.006& 0.011\\ N & 0.017& 0.009& 0.009& 0.002\\ P & 0.018& 0.009& 0.006& 0.002\\ Q & 0.017& 0.008& 0.008& 0.002\\ R & 0.020& 0.010& 0.009& 0.002\\ \hline S & 0.029& 0.016& 0.014& 0.004\\ T & 0.048& 0.027& 0.012& 0.012\\ \bf V &\bf 0.188&\bf 0.227&\bf 0.177&\bf 0.248\\ W & 0.006& 0.003& 0.002& 0.001\\ Y & 0.024& 0.011& 0.006& 0.003\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 11.8449 bits % Probabilities for the components of 9-comp: % 0.0101 0.0020 0.0005 0.0009 0.0577 0.9012 0.0006 0.0238 0.0033 % encoding cost (-log2(probability(column)) with 9-comp is 10.0422 bits % For 5 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 5 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.032& 0.014& 0.014\\ C & 0.019& 0.009& 0.003& 0.004\\ D & 0.020& 0.007& 0.008& 0.002\\ E & 0.021& 0.011& 0.009& 0.002\\ F & 0.044& 0.024& 0.006& 0.007\\ \hline G & 0.023& 0.011& 0.010& 0.002\\ H & 0.010& 0.005& 0.004& 0.001\\ \bf I &\bf 0.235&\bf 0.449&\bf 0.708&\bf 0.673\\ K & 0.028& 0.012& 0.009& 0.002\\ \bf L &\bf 0.141&\bf 0.111&\bf 0.014&\bf 0.038\\ \hline M & 0.036& 0.025& 0.005& 0.010\\ N & 0.017& 0.009& 0.008& 0.002\\ P & 0.018& 0.008& 0.005& 0.002\\ Q & 0.017& 0.008& 0.007& 0.002\\ R & 0.020& 0.010& 0.008& 0.002\\ \hline S & 0.029& 0.016& 0.012& 0.004\\ T & 0.048& 0.027& 0.010& 0.010\\ \bf V &\bf 0.186&\bf 0.214&\bf 0.152&\bf 0.220\\ W & 0.006& 0.003& 0.002& 0.001\\ Y & 0.024& 0.011& 0.005& 0.002\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 12.4438 bits % Probabilities for the components of 9-comp: % 0.0104 0.0020 0.0003 0.0008 0.0558 0.9088 0.0005 0.0172 0.0041 % encoding cost (-log2(probability(column)) with 9-comp is 10.7123 bits % For 6 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 6 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.031& 0.012& 0.012\\ C & 0.019& 0.008& 0.003& 0.004\\ D & 0.020& 0.007& 0.007& 0.001\\ E & 0.021& 0.011& 0.008& 0.002\\ F & 0.044& 0.024& 0.006& 0.006\\ \hline G & 0.023& 0.011& 0.009& 0.002\\ H & 0.010& 0.005& 0.004& 0.001\\ \bf I &\bf 0.237&\bf 0.458&\bf 0.743&\bf 0.708\\ K & 0.028& 0.012& 0.008& 0.002\\ \bf L &\bf 0.142&\bf 0.112&\bf 0.012&\bf 0.034\\ \hline M & 0.036& 0.025& 0.004& 0.009\\ N & 0.017& 0.009& 0.007& 0.002\\ P & 0.018& 0.008& 0.005& 0.002\\ Q & 0.017& 0.008& 0.006& 0.001\\ R & 0.020& 0.010& 0.007& 0.002\\ \hline S & 0.029& 0.015& 0.010& 0.003\\ T & 0.048& 0.027& 0.009& 0.009\\ \bf V &\bf 0.183&\bf 0.204&\bf 0.133&\bf 0.197\\ W & 0.006& 0.003& 0.002& 0.001\\ Y & 0.024& 0.011& 0.004& 0.002\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 12.9427 bits % Probabilities for the components of 9-comp: % 0.0108 0.0020 0.0002 0.0008 0.0543 0.9134 0.0005 0.0129 0.0050 % encoding cost (-log2(probability(column)) with 9-comp is 11.2833 bits % For 7 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 7 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.031& 0.011& 0.011\\ C & 0.019& 0.008& 0.002& 0.003\\ D & 0.020& 0.007& 0.006& 0.001\\ E & 0.021& 0.011& 0.007& 0.002\\ F & 0.044& 0.024& 0.005& 0.006\\ \hline G & 0.023& 0.011& 0.008& 0.002\\ H & 0.010& 0.005& 0.003& 0.001\\ \bf I &\bf 0.239&\bf 0.466&\bf 0.771&\bf 0.737\\ K & 0.028& 0.012& 0.007& 0.002\\ \bf L &\bf 0.143&\bf 0.112&\bf 0.011&\bf 0.031\\ \hline M & 0.036& 0.025& 0.004& 0.008\\ N & 0.017& 0.009& 0.006& 0.001\\ P & 0.018& 0.008& 0.004& 0.002\\ Q & 0.017& 0.008& 0.006& 0.001\\ R & 0.020& 0.010& 0.006& 0.001\\ \hline S & 0.028& 0.015& 0.009& 0.003\\ T & 0.048& 0.027& 0.008& 0.008\\ \bf V &\bf 0.182&\bf 0.197&\bf 0.119&\bf 0.178\\ W & 0.006& 0.003& 0.001& 0.001\\ Y & 0.024& 0.011& 0.004& 0.002\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 13.3705 bits % Probabilities for the components of 9-comp: % 0.0112 0.0021 0.0001 0.0007 0.0532 0.9162 0.0005 0.0100 0.0060 % encoding cost (-log2(probability(column)) with 9-comp is 11.781 bits % For 8 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 8 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.030& 0.010& 0.010\\ C & 0.019& 0.008& 0.002& 0.003\\ D & 0.020& 0.007& 0.006& 0.001\\ E & 0.021& 0.011& 0.007& 0.002\\ F & 0.044& 0.025& 0.005& 0.005\\ \hline G & 0.023& 0.011& 0.007& 0.002\\ H & 0.010& 0.005& 0.003& 0.001\\ \bf I &\bf 0.241&\bf 0.472&\bf 0.794&\bf 0.760\\ K & 0.028& 0.012& 0.007& 0.002\\ \bf L &\bf 0.143&\bf 0.113&\bf 0.010&\bf 0.028\\ \hline M & 0.036& 0.025& 0.004& 0.007\\ N & 0.017& 0.009& 0.005& 0.001\\ P & 0.018& 0.008& 0.004& 0.001\\ Q & 0.017& 0.008& 0.005& 0.001\\ R & 0.020& 0.010& 0.006& 0.001\\ \hline S & 0.028& 0.015& 0.008& 0.003\\ T & 0.048& 0.026& 0.007& 0.008\\ \bf V &\bf 0.181&\bf 0.191&\bf 0.107&\bf 0.163\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.004& 0.002\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 13.745 bits % Probabilities for the components of 9-comp: % 0.0117 0.0021 0.0001 0.0007 0.0523 0.9177 0.0005 0.0079 0.0070 % encoding cost (-log2(probability(column)) with 9-comp is 12.2222 bits % For 9 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 9 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.057& 0.030& 0.009& 0.009\\ C & 0.019& 0.008& 0.002& 0.003\\ D & 0.020& 0.007& 0.005& 0.001\\ E & 0.021& 0.011& 0.006& 0.001\\ F & 0.044& 0.025& 0.004& 0.005\\ \hline G & 0.022& 0.011& 0.006& 0.002\\ H & 0.010& 0.005& 0.003& 0.000\\ \bf I &\bf 0.242&\bf 0.476&\bf 0.812&\bf 0.779\\ K & 0.028& 0.012& 0.006& 0.001\\ \bf L &\bf 0.144&\bf 0.113&\bf 0.009&\bf 0.026\\ \hline M & 0.036& 0.025& 0.003& 0.007\\ N & 0.017& 0.009& 0.005& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.005& 0.001\\ R & 0.020& 0.010& 0.005& 0.001\\ \hline S & 0.028& 0.015& 0.008& 0.002\\ T & 0.048& 0.026& 0.006& 0.007\\ \bf V &\bf 0.180&\bf 0.187&\bf 0.098&\bf 0.150\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.003& 0.002\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 14.0781 bits % Probabilities for the components of 9-comp: % 0.0121 0.0022 0.0001 0.0007 0.0516 0.9185 0.0005 0.0063 0.0081 % encoding cost (-log2(probability(column)) with 9-comp is 12.6185 bits % For 10 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 10 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.030& 0.008& 0.008\\ C & 0.019& 0.008& 0.002& 0.003\\ D & 0.020& 0.006& 0.005& 0.001\\ E & 0.021& 0.011& 0.006& 0.001\\ F & 0.044& 0.025& 0.004& 0.004\\ \hline G & 0.022& 0.011& 0.006& 0.001\\ H & 0.010& 0.005& 0.003& 0.000\\ \bf I &\bf 0.243&\bf 0.480&\bf 0.828&\bf 0.796\\ K & 0.028& 0.012& 0.006& 0.001\\ \bf L &\bf 0.144&\bf 0.114&\bf 0.008&\bf 0.024\\ \hline M & 0.036& 0.025& 0.003& 0.006\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.004& 0.001\\ R & 0.020& 0.010& 0.005& 0.001\\ \hline S & 0.028& 0.015& 0.007& 0.002\\ T & 0.048& 0.026& 0.006& 0.006\\ \bf V &\bf 0.179&\bf 0.183&\bf 0.090&\bf 0.139\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.003& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 14.378 bits % Probabilities for the components of 9-comp: % 0.0125 0.0022 0.0000 0.0006 0.0510 0.9187 0.0005 0.0052 0.0093 % encoding cost (-log2(probability(column)) with 9-comp is 12.9782 bits % For 11 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 11 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.030& 0.008& 0.008\\ C & 0.019& 0.008& 0.002& 0.002\\ D & 0.020& 0.006& 0.004& 0.001\\ E & 0.021& 0.011& 0.005& 0.001\\ F & 0.044& 0.025& 0.004& 0.004\\ \hline G & 0.022& 0.011& 0.005& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.244&\bf 0.483&\bf 0.841&\bf 0.810\\ K & 0.028& 0.012& 0.005& 0.001\\ \bf L &\bf 0.144&\bf 0.114&\bf 0.008&\bf 0.022\\ \hline M & 0.036& 0.026& 0.003& 0.006\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.004& 0.001\\ R & 0.020& 0.010& 0.004& 0.001\\ \hline S & 0.028& 0.015& 0.006& 0.002\\ T & 0.048& 0.026& 0.005& 0.006\\ \bf V &\bf 0.178&\bf 0.180&\bf 0.083&\bf 0.129\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.003& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 14.6508 bits % Probabilities for the components of 9-comp: % 0.0130 0.0023 0.0000 0.0006 0.0504 0.9184 0.0005 0.0043 0.0105 % encoding cost (-log2(probability(column)) with 9-comp is 13.3074 bits % For 12 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 12 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.030& 0.007& 0.007\\ C & 0.019& 0.008& 0.002& 0.002\\ D & 0.020& 0.006& 0.004& 0.001\\ E & 0.021& 0.011& 0.005& 0.001\\ F & 0.044& 0.025& 0.003& 0.004\\ \hline G & 0.022& 0.011& 0.005& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.245&\bf 0.486&\bf 0.852&\bf 0.823\\ K & 0.028& 0.012& 0.005& 0.001\\ \bf L &\bf 0.144&\bf 0.114&\bf 0.007&\bf 0.020\\ \hline M & 0.036& 0.026& 0.003& 0.005\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.004& 0.001\\ R & 0.020& 0.010& 0.004& 0.001\\ \hline S & 0.028& 0.015& 0.006& 0.002\\ T & 0.048& 0.026& 0.005& 0.006\\ \bf V &\bf 0.178&\bf 0.177&\bf 0.077&\bf 0.121\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.003& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 14.901 bits % Probabilities for the components of 9-comp: % 0.0134 0.0023 0.0000 0.0006 0.0499 0.9179 0.0005 0.0036 0.0118 % encoding cost (-log2(probability(column)) with 9-comp is 13.611 bits % For 13 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 13 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.029& 0.007& 0.007\\ C & 0.019& 0.008& 0.001& 0.002\\ D & 0.020& 0.006& 0.004& 0.001\\ E & 0.021& 0.011& 0.004& 0.001\\ F & 0.044& 0.025& 0.003& 0.003\\ \hline G & 0.022& 0.011& 0.005& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.245&\bf 0.488&\bf 0.862&\bf 0.834\\ K & 0.028& 0.012& 0.004& 0.001\\ \bf L &\bf 0.145&\bf 0.114&\bf 0.007&\bf 0.019\\ \hline M & 0.037& 0.026& 0.002& 0.005\\ N & 0.017& 0.009& 0.004& 0.001\\ P & 0.018& 0.008& 0.003& 0.001\\ Q & 0.016& 0.008& 0.003& 0.001\\ R & 0.020& 0.010& 0.004& 0.001\\ \hline S & 0.028& 0.015& 0.006& 0.002\\ T & 0.048& 0.026& 0.005& 0.005\\ \bf V &\bf 0.177&\bf 0.175&\bf 0.072&\bf 0.114\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 15.132 bits % Probabilities for the components of 9-comp: % 0.0138 0.0023 0.0000 0.0006 0.0495 0.9171 0.0005 0.0031 0.0132 % encoding cost (-log2(probability(column)) with 9-comp is 13.8926 bits % For 14 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 14 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.029& 0.006& 0.006\\ C & 0.019& 0.008& 0.001& 0.002\\ D & 0.020& 0.006& 0.004& 0.001\\ E & 0.021& 0.011& 0.004& 0.001\\ F & 0.044& 0.025& 0.003& 0.003\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.246&\bf 0.490&\bf 0.870&\bf 0.843\\ K & 0.028& 0.012& 0.004& 0.001\\ \bf L &\bf 0.145&\bf 0.115&\bf 0.006&\bf 0.018\\ \hline M & 0.037& 0.026& 0.002& 0.005\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.001\\ R & 0.020& 0.010& 0.004& 0.001\\ \hline S & 0.028& 0.015& 0.005& 0.002\\ T & 0.048& 0.026& 0.004& 0.005\\ \bf V &\bf 0.177&\bf 0.173&\bf 0.067&\bf 0.107\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 15.3467 bits % Probabilities for the components of 9-comp: % 0.0142 0.0024 0.0000 0.0006 0.0491 0.9161 0.0004 0.0026 0.0146 % encoding cost (-log2(probability(column)) with 9-comp is 14.1551 bits % For 15 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 15 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.029& 0.006& 0.006\\ C & 0.019& 0.008& 0.001& 0.002\\ D & 0.020& 0.006& 0.003& 0.001\\ E & 0.021& 0.011& 0.004& 0.001\\ F & 0.044& 0.025& 0.003& 0.003\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.246&\bf 0.492&\bf 0.878&\bf 0.852\\ K & 0.028& 0.012& 0.004& 0.001\\ \bf L &\bf 0.145&\bf 0.115&\bf 0.006&\bf 0.017\\ \hline M & 0.037& 0.026& 0.002& 0.004\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.001\\ R & 0.020& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.005& 0.002\\ T & 0.048& 0.026& 0.004& 0.005\\ \bf V &\bf 0.177&\bf 0.171&\bf 0.063&\bf 0.101\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 15.547 bits % Probabilities for the components of 9-comp: % 0.0146 0.0024 0.0000 0.0005 0.0487 0.9150 0.0004 0.0023 0.0160 % encoding cost (-log2(probability(column)) with 9-comp is 14.4009 bits % For 16 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 16 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.029& 0.006& 0.006\\ C & 0.019& 0.008& 0.001& 0.002\\ D & 0.020& 0.006& 0.003& 0.001\\ E & 0.021& 0.011& 0.004& 0.001\\ F & 0.044& 0.025& 0.003& 0.003\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.247&\bf 0.493&\bf 0.885&\bf 0.860\\ K & 0.028& 0.012& 0.004& 0.001\\ \bf L &\bf 0.145&\bf 0.115&\bf 0.005&\bf 0.016\\ \hline M & 0.037& 0.026& 0.002& 0.004\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.001\\ R & 0.020& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.005& 0.002\\ T & 0.048& 0.026& 0.004& 0.004\\ \bf V &\bf 0.176&\bf 0.170&\bf 0.060&\bf 0.096\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 15.735 bits % Probabilities for the components of 9-comp: % 0.0150 0.0025 0.0000 0.0005 0.0484 0.9137 0.0004 0.0020 0.0175 % encoding cost (-log2(probability(column)) with 9-comp is 14.6321 bits % For 17 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 17 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.029& 0.005& 0.005\\ C & 0.019& 0.008& 0.001& 0.002\\ D & 0.020& 0.006& 0.003& 0.001\\ E & 0.021& 0.011& 0.004& 0.001\\ F & 0.044& 0.025& 0.002& 0.003\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.247&\bf 0.494&\bf 0.891&\bf 0.867\\ K & 0.028& 0.012& 0.004& 0.001\\ \bf L &\bf 0.145&\bf 0.115&\bf 0.005&\bf 0.015\\ \hline M & 0.037& 0.026& 0.002& 0.004\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.001\\ R & 0.019& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.004& 0.001\\ T & 0.048& 0.026& 0.004& 0.004\\ \bf V &\bf 0.176&\bf 0.168&\bf 0.057&\bf 0.091\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 15.9119 bits % Probabilities for the components of 9-comp: % 0.0153 0.0025 0.0000 0.0005 0.0481 0.9123 0.0004 0.0017 0.0191 % encoding cost (-log2(probability(column)) with 9-comp is 14.8502 bits % For 18 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 18 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.029& 0.005& 0.005\\ C & 0.019& 0.008& 0.001& 0.002\\ D & 0.020& 0.006& 0.003& 0.001\\ E & 0.021& 0.011& 0.003& 0.001\\ F & 0.044& 0.025& 0.002& 0.003\\ \hline G & 0.022& 0.011& 0.004& 0.001\\ H & 0.010& 0.005& 0.002& 0.000\\ \bf I &\bf 0.247&\bf 0.496&\bf 0.896&\bf 0.873\\ K & 0.028& 0.012& 0.003& 0.001\\ \bf L &\bf 0.145&\bf 0.115&\bf 0.005&\bf 0.014\\ \hline M & 0.037& 0.026& 0.002& 0.004\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.003& 0.001\\ R & 0.019& 0.010& 0.003& 0.001\\ \hline S & 0.028& 0.015& 0.004& 0.001\\ T & 0.048& 0.026& 0.004& 0.004\\ \bf V &\bf 0.176&\bf 0.167&\bf 0.054&\bf 0.087\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 16.079 bits % Probabilities for the components of 9-comp: % 0.0157 0.0025 0.0000 0.0005 0.0478 0.9108 0.0004 0.0015 0.0207 % encoding cost (-log2(probability(column)) with 9-comp is 15.0566 bits % For 19 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 19 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.029& 0.005& 0.005\\ C & 0.019& 0.008& 0.001& 0.002\\ D & 0.020& 0.006& 0.003& 0.001\\ E & 0.020& 0.011& 0.003& 0.001\\ F & 0.044& 0.025& 0.002& 0.002\\ \hline G & 0.022& 0.011& 0.003& 0.001\\ H & 0.010& 0.005& 0.001& 0.000\\ \bf I &\bf 0.248&\bf 0.497&\bf 0.901&\bf 0.879\\ K & 0.028& 0.012& 0.003& 0.001\\ \bf L &\bf 0.145&\bf 0.115&\bf 0.005&\bf 0.014\\ \hline M & 0.037& 0.026& 0.002& 0.004\\ N & 0.017& 0.009& 0.003& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.002& 0.001\\ R & 0.019& 0.010& 0.003& 0.001\\ \hline S & 0.027& 0.015& 0.004& 0.001\\ T & 0.048& 0.026& 0.003& 0.004\\ \bf V &\bf 0.176&\bf 0.166&\bf 0.051&\bf 0.083\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 16.2374 bits % Probabilities for the components of 9-comp: % 0.0161 0.0026 0.0000 0.0005 0.0475 0.9092 0.0004 0.0013 0.0223 % encoding cost (-log2(probability(column)) with 9-comp is 15.2525 bits % For 20 isoleucines and one valine, probabilities are: \begin{table} \begin{center} \begin{tabular}{|l|l|l|l|l|} \hline &\multicolumn{4}{c|}{probabilities given 20 Isoleucines, 1 Valine} \\ \hline &\multicolumn{1}{c|}{GribskovReg}&\multicolumn{1}{c|}{SubstPseudoReg}&\multicolumn{2}{c|}{DirichletReg}\\ \hline & blosum62& subst& 1\-comp& 9\-comp\\ \hline A & 0.056& 0.029& 0.005& 0.005\\ C & 0.019& 0.008& 0.001& 0.002\\ D & 0.020& 0.006& 0.003& 0.001\\ E & 0.020& 0.011& 0.003& 0.001\\ F & 0.044& 0.025& 0.002& 0.002\\ \hline G & 0.022& 0.011& 0.003& 0.001\\ H & 0.010& 0.005& 0.001& 0.000\\ \bf I &\bf 0.248&\bf 0.498&\bf 0.905&\bf 0.884\\ K & 0.028& 0.012& 0.003& 0.001\\ \bf L &\bf 0.145&\bf 0.115&\bf 0.004&\bf 0.013\\ \hline M & 0.037& 0.026& 0.002& 0.003\\ N & 0.017& 0.009& 0.002& 0.001\\ P & 0.018& 0.008& 0.002& 0.001\\ Q & 0.016& 0.008& 0.002& 0.001\\ R & 0.019& 0.010& 0.003& 0.001\\ \hline S & 0.027& 0.015& 0.004& 0.001\\ T & 0.048& 0.026& 0.003& 0.004\\ \bf V &\bf 0.175&\bf 0.165&\bf 0.049&\bf 0.079\\ W & 0.006& 0.003& 0.001& 0.000\\ Y & 0.024& 0.011& 0.002& 0.001\\ \hline \end{tabular} \end{center} \end{table} \clearpage % Probabilities for the components of 1-comp: % 1.0000 % encoding cost (-log2(probability(column)) with 1-comp is 16.3879 bits % Probabilities for the components of 9-comp: % 0.0164 0.0026 0.0000 0.0005 0.0473 0.9075 0.0004 0.0012 0.0240 % encoding cost (-log2(probability(column)) with 9-comp is 15.4389 bits