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Table 1 Accuracy and Confidence values of local alignment

From: The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion

Data set   30 PAM    60 PAM  
Matrix Gap open Gap extention Accuracy Confi-dence Gap open Gap extention Accuracy Confi-dence
PAM30 19.0 0.2 0.9672 0.9883 8.0 1.0 0.6768 0.8781
PAM60 16.0 0.2 0.9776 0.9881 14.0 0.2 0.8635 0.9507
PAM120 10.0 0.1 0.9816 0.9876 10.0 0.5 0.9244 0.9519
PAM250 8.0 0.1 0.9821 0.9862 11.0 0.2 0.9353 0.9489
Blosum45 10.0 0.1 0.9803 0.9861 14.0 0.2 0.9246 0.9439
Blosum50 14.0 0.1 0.9802 0.9862 13.0 0.5 0.9227 0.9436
Blosum62 13.0 0.1 0.9802 0.9862 17.0 0.5 0.9216 0.9479
Gonnet250 8.0 0.1 0.9828 0.9862 10.0 0.2 0.9329 0.9437
Gonnet_p 7.0 0.1 0.9852 0.9839 8.0 0.1 0.9390 0.9336
Optima 9.0 0.1 0.9814 0.9861 17.0 0.5 0.9138 0.9421
VTML250 9.0 0.1 0.9808 0.9854 11.0 0.1 0.9293 0.9426
MIQS 10.0 0.1 0.9813 0.9860 12.0 0.2 0.9287 0.9433
Pfasum050 10.0 0.1 0.9808 0.9860 14.0 0.2 0.9271 0.9444
Pfasum100 10.0 0.1 0.9800 0.9864 12.0 0.2 0.9200 0.9452
Crooks 11.0 0.1 0.9777 0.9859 14.0 0.2 0.9098 0.9457
CCF53 10.0 0.2 0.9796 0.9862 12.0 0.2 0.9195 0.9453
Moll60 11.0 0.1 0.9793 0.9862 11.0 0.5 0.9142 0.9440
Johnson 15.0 0.1 0.9795 0.9866 17.0 0.5 0.9139 0.9465
Prlic 16.0 0.1 0.9811 0.9853 21.0 0.1 0.9251 0.9394
Blake 23.0 0.1 0.9797 0.9841 25.0 1.0 0.9188 0.9318
Benner 8.0 0.2 0.9803 0.9834 10.0 0.1 0.9197 0.9316
Miyazawa 15.0 0.1 0.9749 0.9821 17.0 0.2 0.8941 0.9307
Data set   120 PAM    Bali Base  
Matrix Gap open Gap extention Accuracy Confi-dence Gap open Gap extention Accuracy Confi-dence
PAM30 3.0 1.0 0.1648 0.2826 4.0 1.0 0.3207 0.4471
PAM60 4.0 1.0 0.2781 0.4016 3.0 2.0 0.3928 0.5026
PAM120 6.0 1.0 0.5310 0.6969 7.0 0.5 0.4823 0.5624
PAM250 12.0 0.5 0.7251 0.8039 8.0 0.5 0.5427 0.5821
Blosum45 13.0 0.5 0.6514 0.7664 10.0 0.5 0.5621 0.6121
Blosum50 11.0 1.0 0.6244 0.7482 11.0 0.5 0.5494 0.6050
Blosum62 12.0 1.0 0.5794 0.7378 11.0 0.5 0.5375 0.6019
Gonnet250 11.0 0.5 0.7210 0.7769 8.0 1.0 0.5779 0.6103
Gonnet_p 11.0 0.1 0.7659 0.7538 7.0 0.1 0.6433 0.6338
Optima 10.0 0.5 0.6424 0.7352 9.0 0.5 0.5625 0.6107
VTML250 11.0 0.5 0.7212 0.7757 6.0 1.0 0.5719 0.6025
MIQS 12.0 0.5 0.6969 0.7660 9.0 0.5 0.5729 0.6079
Pfasum050 13.0 0.5 0.6731 0.7602 10.0 0.5 0.5668 0.6090
Pfasum100 9.0 0.5 0.5849 0.7343 7.0 0.5 0.5384 0.5958
Crooks 7.0 1.0 0.4902 0.6733 8.0 0.5 0.5206 0.5958
CCF53 9.0 0.5 0.5819 0.7395 8.0 0.2 0.5358 0.5980
Moll60 7.0 1.0 0.5314 0.6721 8.0 0.5 0.5289 0.6003
Johnson 8.0 2.0 0.4898 0.6623 12.0 0.5 0.5122 0.5917
Prlic 19.0 1.0 0.6714 0.7377 16.0 1.0 0.5741 0.6098
Blake 25.0 4.0 0.6781 0.7396 21.0 1.0 0.5762 0.6016
Benner 12.0 0.5 0.6296 0.6877 8.0 0.5 0.5215 0.5480
Miyazawa 11.0 1.0 0.4928 0.6324 10.0 1.0 0.4826 0.5395