4 /* -------------------------------------------------------------------------- */
6 /* BinCode: 'B' ... RNA sequences, but RY-distance only */
8 char StrEdit_BinCodeA[6] = "_GCAU";
10 float StrEdit_BinCodeM[5][5] =
11 { { 5., 1., 1., 1., 1. }, /* _ */
12 { 1., 0., 1., 0., 1. }, /* G */
13 { 1., 1., 0., 1., 0. }, /* C */
14 { 1., 0., 1., 0., 1. }, /* A */
15 { 1., 1., 0., 1., 0. } }; /* U */
17 /* -------------------------------------------------------------------------- */
19 /* Dayhoff: 'D' ... Dayhoff's matrix for Amino Acids */
20 /* CAUTION THIS IS A SIMILARITY MATRIX !!! */
22 char StrEdit_DayhoffA[22] =
23 "_CSTPAGNDEQHRKMILVFYW";
24 float StrEdit_DayhoffM[21][21] =
25 /* _ C S T P A G N D E Q H R K M I L V F Y W */
26 {{21.,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP}, /* _ ... < ~gap~ > */
27 {GAP,12., 0.,-2.,-3.,-2.,-3.,-4.,-5.,-5.,-5.,-3.,-4.,-5.,-5.,-2.,-6.,-2.,-4., 0.,-8.}, /* C ... Cysteine */
28 {GAP, 0., 2., 1., 1., 1., 1., 1., 0., 0.,-1.,-1., 0., 0.,-2.,-1.,-3.,-1.,-3.,-3.,-2.}, /* S ... Serine */
29 {GAP,-2., 1., 3., 0., 1., 0., 0., 0., 0.,-1.,-1.,-1., 0.,-1., 0.,-2., 0.,-3.,-3.,-5.}, /* T ... Threonine */
30 {GAP,-3., 1., 0., 6., 1.,-1.,-1.,-1.,-1., 0., 0., 0.,-1.,-2.,-2.,-3.,-1.,-5.,-5.,-6.}, /* P ... Proline */
31 {GAP,-2., 1., 1., 1., 2., 1., 0., 0., 0., 0.,-1.,-2.,-1.,-1.,-1.,-2., 0.,-4.,-3.,-6.}, /* A ... Alanine */
32 {GAP,-3., 1., 0.,-1., 1., 5., 0., 1., 0.,-1.,-2.,-3.,-2.,-3.,-3.,-4.,-1.,-5.,-5.,-7.}, /* G ... Glycine */
33 {GAP,-4., 1., 0.,-1., 0., 0., 2., 2., 2., 1., 2., 0., 1.,-2.,-2.,-3.,-2.,-4.,-2.,-4.}, /* N ... Asparagine */
34 {GAP,-5., 0., 0.,-1., 0., 1., 2., 4., 3., 2., 1.,-1., 0.,-3.,-2.,-4.,-2.,-6.,-4.,-7.}, /* D ... Aspartic A */
35 {GAP,-5., 0., 0.,-1., 0., 0., 1., 3., 4., 2., 1.,-1., 0.,-2.,-2.,-3.,-2.,-5.,-4.,-7.}, /* E ... Glutamic A */
36 {GAP,-5.,-1.,-1., 0., 0.,-1., 1., 2., 2., 4., 3., 3., 1.,-1.,-2.,-2.,-2.,-5.,-4.,-5.}, /* Q ... Glutamine */
37 {GAP,-3.,-1.,-1., 0.,-1.,-2., 2., 1., 1., 3., 6., 2., 0.,-2.,-2.,-2.,-2.,-2., 0.,-3.}, /* H ... Histidine */
38 {GAP,-4., 0.,-1., 0.,-2.,-3., 0.,-1.,-1., 1., 2., 6., 3., 0.,-2.,-3.,-2.,-4.,-4.,-2.}, /* R ... Arginine */
39 {GAP,-5., 0., 0.,-1.,-1.,-2., 1., 0., 0., 1., 0., 2., 5., 0.,-2.,-3.,-2.,-5.,-4.,-3.}, /* K ... Lysine */
40 {GAP,-5.,-2.,-1.,-2.,-1.,-3.,-2.,-3.,-2.,-1.,-2., 0., 0., 6., 2., 4., 2., 0.,-2.,-4.}, /* M ... Methionine */
41 {GAP,-2.,-1., 0.,-2.,-1.,-3.,-2.,-2.,-2.,-2.,-2.,-2.,-2., 2., 5., 2., 4., 1.,-1.,-5.}, /* I ... Isoleucine */
42 {GAP,-6.,-3.,-2.,-3.,-2.,-4.,-3.,-4.,-3.,-2.,-2.,-3.,-3., 4., 2., 6., 2., 2.,-1.,-2.}, /* L ... Leucine */
43 {GAP,-2.,-1., 0.,-1., 0.,-1.,-2.,-2.,-2.,-2.,-2.,-2.,-2., 2., 4., 2., 4.,-1.,-2.,-6.}, /* V ... Valine */
44 {GAP,-4.,-3.,-3.,-5.,-4.,-5.,-4.,-6.,-5.,-5.,-2.,-4.,-5., 0., 1., 2.,-1., 9., 7., 0.}, /* F ... Phenylalanine */
45 {GAP, 0.,-3.,-3.,-5.,-3.,-5.,-2.,-4.,-4.,-4., 0.,-4.,-4.,-2.,-1.,-1.,-2., 7.,10., 0.}, /* Y ... Tyrosine */
46 {GAP,-8.,-2.,-5.,-6.,-6.,-7.,-4.,-7.,-7.,-5.,-3.,-2.,-2.,-4.,-5.,-2.,-6., 0., 0.,17.}}; /* W ... Tryptophane */
48 /* -------------------------------------------------------------------------- */
50 /* Hogeweg: 'H' ... Hogeweg's matrix for String Edit of Secondary Structures */
52 char StrEdit_HogewegA[6]="_.^()";
53 float StrEdit_HogewegM[5][5] =
55 { { 5., GAP, GAP, GAP, GAP }, /* _ ... <Gap> */
56 { GAP, 0., 1., 1., 1. }, /* . ... unpaired */
57 { GAP, 1., 0., 1., 1. }, /* ^ ... hairpin-unpaired */
58 { GAP, 1., 1., 0., DINF }, /* ( ... paired upstream */
59 { GAP, 1., 1., DINF, 0. } }; /* ) ... paired downstream */
61 /* -------------------------------------------------------------------------- */
63 char StrEdit_GLHA[22] = "_ACDEFGHIKLMNPQRSTVWY";
64 float StrEdit_GLHM[21][21] = {
65 {21.,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP},
66 {GAP, 0.000, .156, .150, .148, .730, .045, .455, .346, .193, .335,
67 1.018, .140, .058, .237, .308, .046, .010, .246, .124, .977}, /* ALA */
68 {GAP, .156, 0.000, .219, .206, .779, .188, .412, .389, .150, .318,
69 .870, .183, .198, .225, .256, .149, .149, .289, .073, .940}, /* CYS */
70 {GAP, .150, .219,0.000, .017, .840, .120, .337, .494, .129, .479,
71 1.071, .047, .114, .122, .206, .108, .157, .395, .194, .963}, /* ASP */
72 {GAP, .148, .206, .017,0.000, .836, .122, .328, .493, .114, .473,
73 1.057, .030, .117, .110, .194, .103, .154, .393, .181, .950}, /* GLU */
74 {GAP, .730, .779, .840, .836,0.000, .753,1.036, .595, .864, .586,
75 1.301, .822, .763, .900, .957, .761, .729, .617, .726, .920}, /* PHE */
76 {GAP, .045, .188, .120, .122, .753,0.000, .444, .376, .193, .377,
77 1.055, .124, .014, .224, .302, .046, .054, .279, .157, .989}, /* GLY */
78 {GAP, .455, .412, .337, .328,1.036, .444,0.000, .785, .279, .718,
79 1.044, .321, .442, .225, .171, .411, .459, .682, .404, .824}, /* HIS */
80 {GAP, .346, .389, .494, .493, .595, .376, .785,0.000, .513, .159,
81 1.006, .485, .385, .575, .631, .391, .340, .103, .385,1.143}, /* ILE */
82 {GAP, .193, .150, .129, .114, .864, .193, .279, .513,0.000, .461,
83 .954, .093, .194, .077, .119, .152, .193, .410, .152, .919}, /* LYS */
84 {GAP, .335, .318, .479, .473, .586, .377, .718, .159, .461,0.000,
85 .872, .456, .389, .530, .571, .372, .327, .142, .319,1.035}, /* LEU */
86 {GAP, 1.018, .870,1.071,1.057,1.301,1.055,1.044,1.006, .954, .872,
87 0.000,1.033,1.065,1.013, .966,1.018,1.010, .977, .921,1.282}, /* MET */
88 {GAP, .140, .183, .047, .030, .822, .124, .321, .485, .093, .456,
89 1.033,0.000, .122, .102, .184, .095, .146, .383, .156, .930}, /* ASN */
90 {GAP, .058, .198, .114, .117, .763, .014, .442, .385, .194, .389,
91 1.065, .122,0.000, .222, .301, .054, .067, .289, .168, .996}, /* PRO */
92 {GAP, .237, .225, .122, .110, .900, .224, .225, .575, .077, .530,
93 1.013, .102, .222,0.000, .086, .192, .241, .472, .216, .910}, /* GLN */
94 {GAP, .308, .256, .206, .194, .957, .302, .171, .631, .119, .571,
95 .966, .184, .301, .086,0.000, .265, .310, .528, .261, .901}, /* ARG */
96 {GAP, .046, .149, .108, .103, .761, .046, .411, .391, .152, .372,
97 1.018, .095, .054, .192, .265,0.000, .051, .289, .117, .963}, /* SER */
98 {GAP, .010, .149, .157, .154, .729, .054, .459, .340, .193, .327,
99 1.010, .146, .067, .241, .310, .051,0.000, .239, .119, .979}, /* THR */
100 {GAP, .246, .289, .395, .393, .617, .279, .682, .103, .410, .142,
101 .977, .383, .289, .472, .528, .289, .239,0.000, .282,1.076}, /* VAL */
102 {GAP, .124, .073, .194, .181, .726, .157, .404, .385, .152, .319,
103 .921, .156, .168, .216, .261, .117, .119, .282,0.000, .893}, /* TRP */
104 {GAP, .977, .940, .963, .950, .920, .989, .824,1.143, .919,1.035,
105 1.282, .930, .996, .910, .901, .963, .979,1.076, .893,0.000}, /* TYR */