> Dayhoff symbol comparison table > Dayhoff, M. O., Schwartz, R. M., and Orcutt, B. C. [1979] > in Atlas of Protein Sequence and Structure, Dayhoff, M. O. Ed, pp.345-352 > (Figure 84), National Biomedical Research Foundation, Washington D.C. > rescaled by adding 8 to each value. > > .TAB file format: > comments lines begin with > > The first true line gives the N symbols : 0 < N < 32 > The symbol can be any ASCII symbol except > control symbols (ASCII < 32), space, *, -, ., >, :, digits (0..9) > lowercase and uppercase letters are identical > the following lines give the upper part of the symmetrical table > the format is free : N * (N+1) values (range 0..255) are read > OTHER LINES (optional) > After the table, a line beginning with an integer value (between 0 and 255) > can give the standard gap value (8 by default). > The last lines allow you to create clusters of homologous symbols, > following this model : > ! I V > This means that the I and V symbols are homologous and will be represented > by ! in the consensus sequence. The symbol representing a cluster must be > chosen from the list given above. > These clusters can be modified in the program and have no effect on the > evaluation of the multiple aligment, but only on the representation of it > (emphasised/highlighted symbol) and on the consensus sequence. > A B C D E F G H I K L M N P Q R S T V W X Y Z 10 8 6 8 8 4 9 7 7 7 6 7 8 9 8 6 9 9 8 2 8 5 8 A 10 4 11 10 3 8 9 6 9 5 6 10 7 9 7 8 8 6 3 8 5 10 B 20 3 3 4 5 5 6 3 2 3 4 5 3 4 8 6 6 0 8 8 3 C 12 11 2 9 9 6 8 4 5 10 7 10 7 8 8 6 1 8 4 11 D 12 3 8 9 6 8 5 6 9 7 10 7 8 8 6 1 8 4 11 E 17 3 6 9 3 10 8 4 3 3 4 5 5 7 8 8 15 3 F 13 6 5 6 4 5 8 7 7 5 9 8 7 1 8 3 7 G 14 6 8 6 6 10 8 11 10 7 7 6 5 8 8 6 H 13 6 10 10 6 6 6 6 7 8 12 3 8 7 6 I 13 5 8 9 7 9 11 8 8 6 5 8 4 8 K 14 12 5 5 6 5 5 6 10 6 8 7 5 L 14 6 6 7 8 6 7 10 4 8 6 6 M 10 7 9 8 9 8 6 4 8 6 9 N 14 8 8 9 8 7 2 8 3 8 P 12 9 7 7 6 3 8 4 11 Q 14 8 7 6 10 8 4 11 R 10 9 7 6 8 5 8 S 11 8 3 8 5 7 T 12 2 8 6 6 V 25 8 8 2 W 8 8 8 X 18 4 Y 11 Z 8 = Default value for the gap penalty ! I V $ L M % F Y # B D E N Q Z