/* Automatically generated using the TurnerParser TurnerParser (c) 2008,2009,2010 Christian Hoener zu Siederdissen, TBI Vienna choener (at) tbi.univie.ac.at The library enabling this can be found at: http://hackage.haskell.org/package/BiobaseVienna the program can be found at: (sorry, not yet) install using cabal: cabal install (sorry, not yet) */ /* Current free energy parameters are summarized in: D.H.Mathews, J. Sabina, M. ZUker, D.H. Turner "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure" JMB, 288, pp 911-940, 1999 Enthalpies taken from: A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker "Coaxial stacking of helices enhances binding of oligoribonucleotides.." PNAS, 91, pp 9218-9222, 1994 D.H. Turner, N. Sugimoto, and S.M. Freier. "RNA Structure Prediction", Ann. Rev. Biophys. Biophys. Chem. 17, 167-192, 1988. John A.Jaeger, Douglas H.Turner, and Michael Zuker. "Improved predictions of secondary structures for RNA", PNAS, 86, 7706-7710, October 1989. L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner "Nearest-Neighbor Parameters for GU Mismatches...." Biochemistry 1991, 30 11124-11132 A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner "Thermodynamic Study of Internal Loops in Oligoribonucleotides..." Biochemistry 1991, 30, 6428--6435 */ #include "energy_const.h" /*@unused@*/ static char rcsid[] = "$Id: energy_par.c,v 1.6 2004/08/12 12:11:57 ivo Exp $"; #define NST 0 /* Energy for nonstandard stacked pairs */ #define DEF -50 /* Default terminal mismatch, used for I */ /* and any non_pairing bases */ #define NSM 0 /* terminal mismatch for non standard pairs */ #define PUBLIC PUBLIC double Tmeasure = 37+K0; /* temperature of param measurements */ //PUBLIC double lxc37=107.9; PUBLIC double lxc37=107.856; PUBLIC int ML_intern37=-90; PUBLIC int ML_interndH=-220; PUBLIC int ML_closing37=930; PUBLIC int ML_closingdH=3000; PUBLIC int ML_BASE37=0; PUBLIC int ML_BASEdH=0; PUBLIC int MAX_NINIO=300; PUBLIC int ninio37=60; PUBLIC int niniodH=320; PUBLIC int TerminalAU37=50; PUBLIC int TerminalAUdH=370; PUBLIC int DuplexInit37=410; PUBLIC int DuplexInitdH=360; PUBLIC int TripleC37=100; PUBLIC int TripleCdH=1860; PUBLIC int MultipleCA37=30; PUBLIC int MultipleCAdH=340; PUBLIC int MultipleCB37=160; PUBLIC int MultipleCBdH=760; PUBLIC int stack37[NBPAIRS+1][NBPAIRS+1] = {{ INF, INF, INF, INF, INF, INF, INF, INF} ,{ INF, -240, -330, -210, -140, -210, -210, -140} ,{ INF, -330, -340, -250, -150, -220, -240, -150} ,{ INF, -210, -250, 130, -50, -140, -130, 130} ,{ INF, -140, -150, -50, 30, -60, -100, 30} ,{ INF, -210, -220, -140, -60, -110, -90, -60} ,{ INF, -210, -240, -130, -100, -90, -130, -90} ,{ INF, -140, -150, 130, 30, -60, -90, 130}}; PUBLIC int stackdH[NBPAIRS+1][NBPAIRS+1] = {{ INF, INF, INF, INF, INF, INF, INF, INF} ,{ INF, -1060, -1340, -1210, -560, -1050, -1040, -560} ,{ INF, -1340, -1490, -1260, -830, -1140, -1240, -830} ,{ INF, -1210, -1260, -1460, -1350, -880, -1280, -880} ,{ INF, -560, -830, -1350, -930, -320, -700, -320} ,{ INF, -1050, -1140, -880, -320, -940, -680, -320} ,{ INF, -1040, -1240, -1280, -700, -680, -770, -680} ,{ INF, -560, -830, -880, -320, -320, -680, -320}}; PUBLIC int hairpin37[31] = { INF, INF, INF, 540, 560, 570, 540, 600, 550, 640, 650, 660, 670, 680, 690, 690, 700, 710, 710, 720, 720, 730, 730, 740, 740, 750, 750, 750, 760, 760, 770}; PUBLIC int hairpindH[31] = { INF, INF, INF, 130, 480, 360, -290, 130, -290, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500, 500}; PUBLIC int bulge37[31] = { INF, 380, 280, 320, 360, 400, 440, 460, 470, 480, 490, 500, 510, 520, 530, 540, 540, 550, 550, 560, 570, 570, 580, 580, 580, 590, 590, 600, 600, 600, 610}; PUBLIC int bulgedH[31] = { INF, 1060, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710, 710}; PUBLIC int internal_loop37[31] = { INF, INF, INF, INF, 110, 200, 200, 210, 230, 240, 250, 260, 270, 280, 290, 290, 300, 310, 310, 320, 330, 330, 340, 340, 350, 350, 350, 360, 360, 370, 370}; PUBLIC int internal_loopdH[31] = { INF, INF, INF, INF, -720, -680, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130, -130}; PUBLIC int mismatchI37[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, -80, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, -100, 0, -100, 0} ,{ 0, 0, 0, 0, -60} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, -80, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, -100, 0, -100, 0} ,{ 0, 0, 0, 0, -60} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, -10, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -30, 70, -30, 70} ,{ 70, 70, 70, 70, 10} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, -10, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -30, 70, -30, 70} ,{ 70, 70, 70, 70, 10} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, -10, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -30, 70, -30, 70} ,{ 70, 70, 70, 70, 10} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, -10, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -30, 70, -30, 70} ,{ 70, 70, 70, 70, 10} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, -10, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -30, 70, -30, 70} ,{ 70, 70, 70, 70, 10} }}; PUBLIC int mismatchIdH[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ 280, 0, 0, 280, 0} ,{ 0, 0, 0, -340, 0} ,{ 0, 0, 0, 0, 0} ,{ 280, -760, 0, 280, 0} ,{ 0, 0, 0, 0, -580} } ,{{ 280, 0, 0, 280, 0} ,{ 0, 0, 0, -340, 0} ,{ 0, 0, 0, 0, 0} ,{ 280, -760, 0, 280, 0} ,{ 0, 0, 0, 0, -580} } ,{{ 790, 500, 500, 790, 500} ,{ 500, 500, 500, 170, 500} ,{ 500, 500, 500, 500, 500} ,{ 790, -260, 500, 790, 500} ,{ 500, 500, 500, 500, -80} } ,{{ 790, 500, 500, 790, 500} ,{ 500, 500, 500, 170, 500} ,{ 500, 500, 500, 500, 500} ,{ 790, -260, 500, 790, 500} ,{ 500, 500, 500, 500, -80} } ,{{ 790, 500, 500, 790, 500} ,{ 500, 500, 500, 170, 500} ,{ 500, 500, 500, 500, 500} ,{ 790, -260, 500, 790, 500} ,{ 500, 500, 500, 500, -80} } ,{{ 790, 500, 500, 790, 500} ,{ 500, 500, 500, 170, 500} ,{ 500, 500, 500, 500, 500} ,{ 790, -260, 500, 790, 500} ,{ 500, 500, 500, 500, -80} } ,{{ 790, 500, 500, 790, 500} ,{ 500, 500, 500, 170, 500} ,{ 500, 500, 500, 500, 500} ,{ 790, -260, 500, 790, 500} ,{ 500, 500, 500, 500, -80} }}; PUBLIC int mismatchH37[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ -80, -100, -110, -100, -80} ,{ -140, -150, -150, -140, -150} ,{ -80, -100, -110, -100, -80} ,{ -150, -230, -150, -240, -150} ,{ -100, -100, -140, -100, -210} } ,{{ -50, -110, -70, -110, -50} ,{ -110, -110, -150, -130, -150} ,{ -50, -110, -70, -110, -50} ,{ -150, -250, -150, -220, -150} ,{ -100, -110, -100, -110, -160} } ,{{ 20, 20, -20, -10, -20} ,{ 20, 20, -50, -30, -50} ,{ -10, -10, -20, -10, -20} ,{ -50, -100, -50, -110, -50} ,{ -10, -10, -30, -10, -100} } ,{{ 0, -20, -10, -20, 0} ,{ -30, -50, -30, -60, -30} ,{ 0, -20, -10, -20, 0} ,{ -30, -90, -30, -110, -30} ,{ -10, -20, -10, -20, -90} } ,{{ -10, -10, -20, -10, -20} ,{ -30, -30, -50, -30, -50} ,{ -10, -10, -20, -10, -20} ,{ -50, -120, -50, -110, -50} ,{ -10, -10, -30, -10, -120} } ,{{ 0, -20, -10, -20, 0} ,{ -30, -50, -30, -50, -30} ,{ 0, -20, -10, -20, 0} ,{ -30, -150, -30, -150, -30} ,{ -10, -20, -10, -20, -90} } ,{{ 20, 20, -10, -10, 0} ,{ 20, 20, -30, -30, -30} ,{ 0, -10, -10, -10, 0} ,{ -30, -90, -30, -110, -30} ,{ -10, -10, -10, -10, -90} }}; PUBLIC int mismatchHdH[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ 560, -570, 560, -560, -270} ,{ -560, -910, -560, -560, -560} ,{ -270, -570, -340, -570, -270} ,{ 560, -1400, 560, -920, -560} ,{ -530, -570, -530, -570, -1440} } ,{{ 50, -520, 50, -560, -400} ,{ -400, -520, -400, -560, -400} ,{ 50, -720, 50, -720, -420} ,{ -400, -1290, -400, -620, -400} ,{ -30, -720, -30, -720, -1080} } ,{{ 970, 140, 970, 140, 570} ,{ 570, 30, 570, 20, 570} ,{ 970, 140, 970, 140, 340} ,{ 570, -270, 570, 20, 570} ,{ 830, 140, 830, 140, -50} } ,{{ 230, 100, 230, 220, 190} ,{ -110, -110, -260, -520, -260} ,{ 190, -60, -140, -60, 190} ,{ 220, 100, -260, 220, -260} ,{ 230, -60, 230, -60, -70} } ,{{ 970, 140, 970, 140, 570} ,{ 570, -20, 570, 20, 570} ,{ 970, 140, 970, 140, 340} ,{ 570, -520, 570, 20, 570} ,{ 830, 140, 830, 140, -380} } ,{{ 230, -30, 230, -60, 190} ,{ -30, -30, -260, -520, -260} ,{ 190, -60, -140, -60, 190} ,{ -260, -590, -260, -520, -260} ,{ 230, -60, 230, -60, -70} } ,{{ 970, 140, 970, 220, 570} ,{ 570, 30, 570, 20, 570} ,{ 970, 140, 970, 140, 340} ,{ 570, 100, 570, 220, 570} ,{ 830, 140, 830, 140, -50} }}; PUBLIC int mismatchM37[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ -80, -100, -110, -100, -80} ,{ -140, -150, -150, -140, -150} ,{ -80, -100, -110, -100, -80} ,{ -140, -140, -150, -160, -150} ,{ -100, -100, -140, -100, -120} } ,{{ -50, -110, -70, -110, -50} ,{ -110, -110, -150, -130, -150} ,{ -50, -110, -70, -110, -50} ,{ -140, -160, -150, -140, -150} ,{ -70, -110, -100, -110, -70} } ,{{ -30, -30, -70, -60, -60} ,{ -30, -30, -100, -80, -100} ,{ -60, -60, -70, -60, -70} ,{ -60, -60, -100, -80, -100} ,{ -60, -60, -80, -60, -60} } ,{{ -50, -50, -60, -70, -50} ,{ -80, -100, -80, -110, -80} ,{ -50, -70, -60, -70, -50} ,{ -50, -50, -80, -80, -80} ,{ -50, -70, -60, -70, -50} } ,{{ -60, -60, -70, -60, -70} ,{ -80, -80, -100, -80, -100} ,{ -60, -60, -70, -60, -70} ,{ -80, -80, -100, -80, -100} ,{ -60, -60, -80, -60, -80} } ,{{ -50, -70, -60, -70, -50} ,{ -80, -100, -80, -110, -80} ,{ -50, -70, -60, -70, -50} ,{ -80, -110, -80, -120, -80} ,{ -50, -70, -60, -70, -50} } ,{{ -30, -30, -60, -60, -50} ,{ -30, -30, -80, -80, -80} ,{ -50, -60, -60, -60, -50} ,{ -50, -50, -80, -80, -80} ,{ -50, -60, -60, -60, -50} }}; PUBLIC int mismatchMdH[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ -270, -570, -340, -560, -270} ,{ -560, -910, -560, -560, -560} ,{ -270, -570, -340, -570, -270} ,{ -560, -820, -560, -920, -560} ,{ -530, -570, -530, -570, -860} } ,{{ 50, -520, 50, -560, -400} ,{ -400, -520, -400, -560, -400} ,{ 50, -720, 50, -720, -420} ,{ -400, -710, -400, -620, -400} ,{ -30, -720, -30, -720, -500} } ,{{ 600, -60, 600, -230, 200} ,{ 200, -340, 200, -350, 200} ,{ 600, -230, 600, -230, -30} ,{ 200, -60, 200, -350, 200} ,{ 460, -230, 460, -230, 160} } ,{{ 310, 310, -140, -150, 140} ,{ -480, -480, -630, -890, -630} ,{ -180, -430, -510, -430, -180} ,{ 310, 310, -630, -150, -630} ,{ 140, -430, -140, -430, 140} } ,{{ 600, -230, 600, -230, 200} ,{ 200, -390, 200, -350, 200} ,{ 600, -230, 600, -230, -30} ,{ 200, -310, 200, -350, 200} ,{ 460, -230, 460, -230, -170} } ,{{ 140, -380, -140, -430, 140} ,{ -400, -400, -630, -890, -630} ,{ -180, -430, -510, -430, -180} ,{ -380, -380, -630, -890, -630} ,{ 140, -430, -140, -430, 140} } ,{{ 600, 310, 600, -150, 200} ,{ 200, -340, 200, -350, 200} ,{ 600, -230, 600, -230, -30} ,{ 310, 310, 200, -150, 200} ,{ 460, -230, 460, -230, 160} }}; PUBLIC int mismatch1nI37[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} }}; PUBLIC int mismatch1nIdH[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} }}; PUBLIC int mismatch23I37[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, -50, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, -110, 0, -70, 0} ,{ 0, 0, 0, 0, -30} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, -120, 0, -70, 0} ,{ 0, 0, 0, 0, -30} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -40, 70, 0, 70} ,{ 70, 70, 70, 70, 40} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 20, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -40, 70, 0, 70} ,{ 70, 70, 70, 70, 40} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -40, 70, 0, 70} ,{ 70, 70, 70, 70, 40} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 20, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -40, 70, 0, 70} ,{ 70, 70, 70, 70, 40} } ,{{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, 70, 70, 70, 70} ,{ 70, -40, 70, 0, 70} ,{ 70, 70, 70, 70, 40} }}; PUBLIC int mismatch23IdH[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, -570, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, -860, 0, -900, 0} ,{ 0, 0, 0, 0, -640} } ,{{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, 0, 0, 0, 0} ,{ 0, -1090, 0, -900, 0} ,{ 0, 0, 0, 0, -640} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, -580, 500, -400, 500} ,{ 500, 500, 500, 500, -140} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, -60, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, -360, 500, -400, 500} ,{ 500, 500, 500, 500, -140} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, -580, 500, -400, 500} ,{ 500, 500, 500, 500, -140} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, -60, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, -360, 500, -400, 500} ,{ 500, 500, 500, 500, -140} } ,{{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, 500, 500, 500, 500} ,{ 500, -360, 500, -400, 500} ,{ 500, 500, 500, 500, -140} }}; PUBLIC int mismatchExt37[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ -80, -100, -110, -100, -80} ,{ -140, -150, -150, -140, -150} ,{ -80, -100, -110, -100, -80} ,{ -140, -140, -150, -160, -150} ,{ -100, -100, -140, -100, -120} } ,{{ -50, -110, -70, -110, -50} ,{ -110, -110, -150, -130, -150} ,{ -50, -110, -70, -110, -50} ,{ -140, -160, -150, -140, -150} ,{ -70, -110, -100, -110, -70} } ,{{ -30, -30, -70, -60, -60} ,{ -30, -30, -100, -80, -100} ,{ -60, -60, -70, -60, -70} ,{ -60, -60, -100, -80, -100} ,{ -60, -60, -80, -60, -60} } ,{{ -50, -50, -60, -70, -50} ,{ -80, -100, -80, -110, -80} ,{ -50, -70, -60, -70, -50} ,{ -50, -50, -80, -80, -80} ,{ -50, -70, -60, -70, -50} } ,{{ -60, -60, -70, -60, -70} ,{ -80, -80, -100, -80, -100} ,{ -60, -60, -70, -60, -70} ,{ -80, -80, -100, -80, -100} ,{ -60, -60, -80, -60, -80} } ,{{ -50, -70, -60, -70, -50} ,{ -80, -100, -80, -110, -80} ,{ -50, -70, -60, -70, -50} ,{ -80, -110, -80, -120, -80} ,{ -50, -70, -60, -70, -50} } ,{{ -30, -30, -60, -60, -50} ,{ -30, -30, -80, -80, -80} ,{ -50, -60, -60, -60, -50} ,{ -50, -50, -80, -80, -80} ,{ -50, -60, -60, -60, -50} }}; PUBLIC int mismatchExtdH[NBPAIRS+1][5][5] = {{{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} ,{ INF, INF, INF, INF, INF} } ,{{ -270, -570, -340, -560, -270} ,{ -560, -910, -560, -560, -560} ,{ -270, -570, -340, -570, -270} ,{ -560, -820, -560, -920, -560} ,{ -530, -570, -530, -570, -860} } ,{{ 50, -520, 50, -560, -400} ,{ -400, -520, -400, -560, -400} ,{ 50, -720, 50, -720, -420} ,{ -400, -710, -400, -620, -400} ,{ -30, -720, -30, -720, -500} } ,{{ 600, -60, 600, -230, 200} ,{ 200, -340, 200, -350, 200} ,{ 600, -230, 600, -230, -30} ,{ 200, -60, 200, -350, 200} ,{ 460, -230, 460, -230, 160} } ,{{ 310, 310, -140, -150, 140} ,{ -480, -480, -630, -890, -630} ,{ -180, -430, -510, -430, -180} ,{ 310, 310, -630, -150, -630} ,{ 140, -430, -140, -430, 140} } ,{{ 600, -230, 600, -230, 200} ,{ 200, -390, 200, -350, 200} ,{ 600, -230, 600, -230, -30} ,{ 200, -310, 200, -350, 200} ,{ 460, -230, 460, -230, -170} } ,{{ 140, -380, -140, -430, 140} ,{ -400, -400, -630, -890, -630} ,{ -180, -430, -510, -430, -180} ,{ -380, -380, -630, -890, -630} ,{ 140, -430, -140, -430, 140} } ,{{ 600, 310, 600, -150, 200} ,{ 200, -340, 200, -350, 200} ,{ 600, -230, 600, -230, -30} ,{ 310, 310, 200, -150, 200} ,{ 460, -230, 460, -230, 160} }}; PUBLIC int dangle3_37[NBPAIRS+1][5] = {{ INF, INF, INF, INF, INF} ,{ -80, -170, -80, -170, -120} ,{ -40, -110, -40, -130, -60} ,{ -50, -80, -50, -80, -60} ,{ -10, -70, -10, -70, -10} ,{ -50, -80, -50, -80, -60} ,{ -10, -70, -10, -70, -10} ,{ -10, -70, -10, -70, -10}}; PUBLIC int dangle3_dH[NBPAIRS+1][5] = {{ INF, INF, INF, INF, INF} ,{ -410, -900, -410, -860, -750} ,{ -280, -740, -280, -640, -360} ,{ -90, -490, -90, -550, -230} ,{ -70, -570, -70, -580, -220} ,{ -90, -490, -90, -550, -230} ,{ -70, -570, -70, -580, -220} ,{ -70, -490, -70, -550, -220}}; PUBLIC int dangle5_37[NBPAIRS+1][5] = {{ INF, INF, INF, INF, INF} ,{ 0, -20, -30, 0, 0} ,{ -10, -50, -30, -20, -10} ,{ -10, -30, -10, -20, -20} ,{ -20, -30, -30, -40, -20} ,{ -10, -30, -10, -20, -20} ,{ -20, -30, -30, -40, -20} ,{ 0, -20, -10, 0, 0}}; PUBLIC int dangle5_dH[NBPAIRS+1][5] = {{ INF, INF, INF, INF, INF} ,{ 70, -160, 70, -460, -40} ,{ 330, -240, 330, 80, -140} ,{ 690, -50, 690, 60, 60} ,{ 310, 160, 220, 70, 310} ,{ 690, -50, 690, 60, 60} ,{ 310, 160, 220, 70, 310} ,{ 690, 160, 690, 80, 310}}; PUBLIC char Triloops[241] = "CAACG " "GUUAC " ; PUBLIC int Triloop37[40] = { 680, 690}; PUBLIC int TriloopdH[40] = { 2370, 1080}; PUBLIC char Tetraloops[281] = "CAACGG " "CCAAGG " "CCACGG " "CCCAGG " "CCGAGG " "CCGCGG " "CCUAGG " "CCUCGG " "CUAAGG " "CUACGG " "CUCAGG " "CUCCGG " "CUGCGG " "CUUAGG " "CUUCGG " "CUUUGG " ; PUBLIC int Tetraloop37[40] = { 550, 330, 370, 340, 350, 360, 370, 250, 360, 280, 370, 270, 280, 350, 370, 370}; PUBLIC int TetraloopdH[40] = { 690, -1030, -330, -890, -660, -750, -350, -1390, -760, -1070, -660, -1290, -1070, -620, -1530, -680}; PUBLIC char Hexaloops[361] = "ACAGUACU " "ACAGUGAU " "ACAGUGCU " "ACAGUGUU " ; PUBLIC int Hexaloop37[40] = { 280, 360, 290, 180}; PUBLIC int HexaloopdH[40] = { -1680, -1140, -1280, -1540}; #include "intl11.h" #include "intl11dH.h" #include "intl21.h" #include "intl21dH.h" #include "intl22.h" #include "intl22dH.h"