#define DINF 100000.0 #define GAP 1.0 /* -------------------------------------------------------------------------- */ /* BinCode: 'B' ... RNA sequences, but RY-distance only */ char StrEdit_BinCodeA[6] = "_GCAU"; /* _ G C A U */ float StrEdit_BinCodeM[5][5] = { { 5., 1., 1., 1., 1. }, /* _ */ { 1., 0., 1., 0., 1. }, /* G */ { 1., 1., 0., 1., 0. }, /* C */ { 1., 0., 1., 0., 1. }, /* A */ { 1., 1., 0., 1., 0. } }; /* U */ /* -------------------------------------------------------------------------- */ /* Dayhoff: 'D' ... Dayhoff's matrix for Amino Acids */ /* CAUTION THIS IS A SIMILARITY MATRIX !!! */ char StrEdit_DayhoffA[22] = "_CSTPAGNDEQHRKMILVFYW"; float StrEdit_DayhoffM[21][21] = /* _ C S T P A G N D E Q H R K M I L V F Y W */ {{21.,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP}, /* _ ... < ~gap~ > */ {GAP,12., 0.,-2.,-3.,-2.,-3.,-4.,-5.,-5.,-5.,-3.,-4.,-5.,-5.,-2.,-6.,-2.,-4., 0.,-8.}, /* C ... Cysteine */ {GAP, 0., 2., 1., 1., 1., 1., 1., 0., 0.,-1.,-1., 0., 0.,-2.,-1.,-3.,-1.,-3.,-3.,-2.}, /* S ... Serine */ {GAP,-2., 1., 3., 0., 1., 0., 0., 0., 0.,-1.,-1.,-1., 0.,-1., 0.,-2., 0.,-3.,-3.,-5.}, /* T ... Threonine */ {GAP,-3., 1., 0., 6., 1.,-1.,-1.,-1.,-1., 0., 0., 0.,-1.,-2.,-2.,-3.,-1.,-5.,-5.,-6.}, /* P ... Proline */ {GAP,-2., 1., 1., 1., 2., 1., 0., 0., 0., 0.,-1.,-2.,-1.,-1.,-1.,-2., 0.,-4.,-3.,-6.}, /* A ... Alanine */ {GAP,-3., 1., 0.,-1., 1., 5., 0., 1., 0.,-1.,-2.,-3.,-2.,-3.,-3.,-4.,-1.,-5.,-5.,-7.}, /* G ... Glycine */ {GAP,-4., 1., 0.,-1., 0., 0., 2., 2., 2., 1., 2., 0., 1.,-2.,-2.,-3.,-2.,-4.,-2.,-4.}, /* N ... Asparagine */ {GAP,-5., 0., 0.,-1., 0., 1., 2., 4., 3., 2., 1.,-1., 0.,-3.,-2.,-4.,-2.,-6.,-4.,-7.}, /* D ... Aspartic A */ {GAP,-5., 0., 0.,-1., 0., 0., 1., 3., 4., 2., 1.,-1., 0.,-2.,-2.,-3.,-2.,-5.,-4.,-7.}, /* E ... Glutamic A */ {GAP,-5.,-1.,-1., 0., 0.,-1., 1., 2., 2., 4., 3., 3., 1.,-1.,-2.,-2.,-2.,-5.,-4.,-5.}, /* Q ... Glutamine */ {GAP,-3.,-1.,-1., 0.,-1.,-2., 2., 1., 1., 3., 6., 2., 0.,-2.,-2.,-2.,-2.,-2., 0.,-3.}, /* H ... Histidine */ {GAP,-4., 0.,-1., 0.,-2.,-3., 0.,-1.,-1., 1., 2., 6., 3., 0.,-2.,-3.,-2.,-4.,-4.,-2.}, /* R ... Arginine */ {GAP,-5., 0., 0.,-1.,-1.,-2., 1., 0., 0., 1., 0., 2., 5., 0.,-2.,-3.,-2.,-5.,-4.,-3.}, /* K ... Lysine */ {GAP,-5.,-2.,-1.,-2.,-1.,-3.,-2.,-3.,-2.,-1.,-2., 0., 0., 6., 2., 4., 2., 0.,-2.,-4.}, /* M ... Methionine */ {GAP,-2.,-1., 0.,-2.,-1.,-3.,-2.,-2.,-2.,-2.,-2.,-2.,-2., 2., 5., 2., 4., 1.,-1.,-5.}, /* I ... Isoleucine */ {GAP,-6.,-3.,-2.,-3.,-2.,-4.,-3.,-4.,-3.,-2.,-2.,-3.,-3., 4., 2., 6., 2., 2.,-1.,-2.}, /* L ... Leucine */ {GAP,-2.,-1., 0.,-1., 0.,-1.,-2.,-2.,-2.,-2.,-2.,-2.,-2., 2., 4., 2., 4.,-1.,-2.,-6.}, /* V ... Valine */ {GAP,-4.,-3.,-3.,-5.,-4.,-5.,-4.,-6.,-5.,-5.,-2.,-4.,-5., 0., 1., 2.,-1., 9., 7., 0.}, /* F ... Phenylalanine */ {GAP, 0.,-3.,-3.,-5.,-3.,-5.,-2.,-4.,-4.,-4., 0.,-4.,-4.,-2.,-1.,-1.,-2., 7.,10., 0.}, /* Y ... Tyrosine */ {GAP,-8.,-2.,-5.,-6.,-6.,-7.,-4.,-7.,-7.,-5.,-3.,-2.,-2.,-4.,-5.,-2.,-6., 0., 0.,17.}}; /* W ... Tryptophane */ /* -------------------------------------------------------------------------- */ /* Hogeweg: 'H' ... Hogeweg's matrix for String Edit of Secondary Structures */ char StrEdit_HogewegA[6]="_.^()"; float StrEdit_HogewegM[5][5] = /* _ . ^ ( ) */ { { 5., GAP, GAP, GAP, GAP }, /* _ ... */ { GAP, 0., 1., 1., 1. }, /* . ... unpaired */ { GAP, 1., 0., 1., 1. }, /* ^ ... hairpin-unpaired */ { GAP, 1., 1., 0., DINF }, /* ( ... paired upstream */ { GAP, 1., 1., DINF, 0. } }; /* ) ... paired downstream */ /* -------------------------------------------------------------------------- */ char StrEdit_GLHA[22] = "_ACDEFGHIKLMNPQRSTVWY"; float StrEdit_GLHM[21][21] = { {21.,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP,GAP}, {GAP, 0.000, .156, .150, .148, .730, .045, .455, .346, .193, .335, 1.018, .140, .058, .237, .308, .046, .010, .246, .124, .977}, /* ALA */ {GAP, .156, 0.000, .219, .206, .779, .188, .412, .389, .150, .318, .870, .183, .198, .225, .256, .149, .149, .289, .073, .940}, /* CYS */ {GAP, .150, .219,0.000, .017, .840, .120, .337, .494, .129, .479, 1.071, .047, .114, .122, .206, .108, .157, .395, .194, .963}, /* ASP */ {GAP, .148, .206, .017,0.000, .836, .122, .328, .493, .114, .473, 1.057, .030, .117, .110, .194, .103, .154, .393, .181, .950}, /* GLU */ {GAP, .730, .779, .840, .836,0.000, .753,1.036, .595, .864, .586, 1.301, .822, .763, .900, .957, .761, .729, .617, .726, .920}, /* PHE */ {GAP, .045, .188, .120, .122, .753,0.000, .444, .376, .193, .377, 1.055, .124, .014, .224, .302, .046, .054, .279, .157, .989}, /* GLY */ {GAP, .455, .412, .337, .328,1.036, .444,0.000, .785, .279, .718, 1.044, .321, .442, .225, .171, .411, .459, .682, .404, .824}, /* HIS */ {GAP, .346, .389, .494, .493, .595, .376, .785,0.000, .513, .159, 1.006, .485, .385, .575, .631, .391, .340, .103, .385,1.143}, /* ILE */ {GAP, .193, .150, .129, .114, .864, .193, .279, .513,0.000, .461, .954, .093, .194, .077, .119, .152, .193, .410, .152, .919}, /* LYS */ {GAP, .335, .318, .479, .473, .586, .377, .718, .159, .461,0.000, .872, .456, .389, .530, .571, .372, .327, .142, .319,1.035}, /* LEU */ {GAP, 1.018, .870,1.071,1.057,1.301,1.055,1.044,1.006, .954, .872, 0.000,1.033,1.065,1.013, .966,1.018,1.010, .977, .921,1.282}, /* MET */ {GAP, .140, .183, .047, .030, .822, .124, .321, .485, .093, .456, 1.033,0.000, .122, .102, .184, .095, .146, .383, .156, .930}, /* ASN */ {GAP, .058, .198, .114, .117, .763, .014, .442, .385, .194, .389, 1.065, .122,0.000, .222, .301, .054, .067, .289, .168, .996}, /* PRO */ {GAP, .237, .225, .122, .110, .900, .224, .225, .575, .077, .530, 1.013, .102, .222,0.000, .086, .192, .241, .472, .216, .910}, /* GLN */ {GAP, .308, .256, .206, .194, .957, .302, .171, .631, .119, .571, .966, .184, .301, .086,0.000, .265, .310, .528, .261, .901}, /* ARG */ {GAP, .046, .149, .108, .103, .761, .046, .411, .391, .152, .372, 1.018, .095, .054, .192, .265,0.000, .051, .289, .117, .963}, /* SER */ {GAP, .010, .149, .157, .154, .729, .054, .459, .340, .193, .327, 1.010, .146, .067, .241, .310, .051,0.000, .239, .119, .979}, /* THR */ {GAP, .246, .289, .395, .393, .617, .279, .682, .103, .410, .142, .977, .383, .289, .472, .528, .289, .239,0.000, .282,1.076}, /* VAL */ {GAP, .124, .073, .194, .181, .726, .157, .404, .385, .152, .319, .921, .156, .168, .216, .261, .117, .119, .282,0.000, .893}, /* TRP */ {GAP, .977, .940, .963, .950, .920, .989, .824,1.143, .919,1.035, 1.282, .930, .996, .910, .901, .963, .979,1.076, .893,0.000}, /* TYR */ };