#include "common.h"#include "oligoTm.h"Include dependency graph for oligoTm.c:
Go to the source code of this file.
Defines | |
| #define | S_A_A 240 |
| #define | S_A_C 173 |
| #define | S_A_G 208 |
| #define | S_A_T 239 |
| #define | S_A_N 215 |
| #define | S_C_A 129 |
| #define | S_C_C 266 |
| #define | S_C_G 278 |
| #define | S_C_T 208 |
| #define | S_C_N 220 |
| #define | S_G_A 135 |
| #define | S_G_C 267 |
| #define | S_G_G 266 |
| #define | S_G_T 173 |
| #define | S_G_N 210 |
| #define | S_T_A 169 |
| #define | S_T_C 135 |
| #define | S_T_G 129 |
| #define | S_T_T 240 |
| #define | S_T_N 168 |
| #define | S_N_A 168 |
| #define | S_N_C 210 |
| #define | S_N_G 220 |
| #define | S_N_T 215 |
| #define | S_N_N 203 |
| #define | H_A_A 91 |
| #define | H_A_C 65 |
| #define | H_A_G 78 |
| #define | H_A_T 86 |
| #define | H_A_N 80 |
| #define | H_C_A 58 |
| #define | H_C_C 110 |
| #define | H_C_G 119 |
| #define | H_C_T 78 |
| #define | H_C_N 91 |
| #define | H_G_A 56 |
| #define | H_G_C 111 |
| #define | H_G_G 110 |
| #define | H_G_T 65 |
| #define | H_G_N 85 |
| #define | H_T_A 60 |
| #define | H_T_C 56 |
| #define | H_T_G 58 |
| #define | H_T_T 91 |
| #define | H_T_N 66 |
| #define | H_N_A 66 |
| #define | H_N_C 85 |
| #define | H_N_G 91 |
| #define | H_N_T 80 |
| #define | H_N_N 80 |
| #define | G_A_A 1900 |
| #define | G_A_C 1300 |
| #define | G_A_G 1600 |
| #define | G_A_T 1500 |
| #define | G_A_N 1575 |
| #define | G_C_A 1900 |
| #define | G_C_C 3100 |
| #define | G_C_G 3600 |
| #define | G_C_T 1600 |
| #define | G_C_N 2550 |
| #define | G_G_A 1600 |
| #define | G_G_C 3100 |
| #define | G_G_G 3100 |
| #define | G_G_T 1300 |
| #define | G_G_N 2275 |
| #define | G_T_A 900 |
| #define | G_T_C 1600 |
| #define | G_T_G 1900 |
| #define | G_T_T 1900 |
| #define | G_T_N 1575 |
| #define | G_N_A 1575 |
| #define | G_N_C 2275 |
| #define | G_N_G 2550 |
| #define | G_N_T 1575 |
| #define | G_N_N 1994 |
| #define | A_CHAR 'A' |
| #define | G_CHAR 'G' |
| #define | T_CHAR 'T' |
| #define | C_CHAR 'C' |
| #define | N_CHAR 'N' |
| #define | CATID5(A, B, C, D, E) A##B##C##D##E |
| #define | CATID2(A, B) A##B |
| #define | DO_PAIR(LAST, THIS) |
| #define | STATE(LAST) |
| #define | DO_PAIR(LAST, THIS) |
Functions | |
| double | oligoTm (char *dna, double DNA_nM, double K_mM) |
| double | oligoDg (char *dna) |
| double | longSeqTm (char *s, int start, int len, double salt_conc) |
| double | seqTm (char *seq, double dna_conc, double salt_conc) |
| #define DO_PAIR | ( | LAST, | |||
| THIS | ) |
| #define DO_PAIR | ( | LAST, | |||
| THIS | ) |
| #define STATE | ( | LAST | ) |
| double longSeqTm | ( | char * | s, | |
| int | start, | |||
| int | len, | |||
| double | salt_conc | |||
| ) |
Definition at line 282 of file oligoTm.c.
References errAbort().
Referenced by seqTm().
00284 :1390 (1962) as presented in 00285 * Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11.46 (1989, CSHL 00286 * Press). 00287 * 00288 * Tm = 81.5 + 16.6(log10([Na+])) + .41*(%GC) - 600/length 00289 * 00290 * Where [Na+] is the molar sodium concentration, (%GC) is the percent of Gs 00291 * and Cs in the sequence, and length is the length of the sequence. 00292 * 00293 * A similar formula is used by the prime primer selection program in GCG 00294 * (http://www.gcg.com), which instead uses 675.0 / length in the last term 00295 * (after F. Baldino, Jr, M.-F. Chesselet, and M.E. Lewis, Methods in 00296 * Enzymology 168:766 (1989) eqn (1) on page 766 without the mismatch and 00297 * formamide terms). The formulas here and in Baldino et al. assume Na+ rather 00298 * than K+. According to J.G. Wetmur, Critical Reviews in BioChem. and 00299 * Mol. Bio. 26:227 (1991) 50 mM K+ should be equivalent in these formulae to .2 00300 * M Na+. 00301 * 00302 * This function takes salt_conc to be the millimolar (mM) concentration, 00303 * since mM is the usual units in PCR applications. */ 00304 { 00305 int GC_count = 0; 00306 char *p, *end; 00307 00308 if(start + len > strlen(s) || start < 0 || len <= 0) 00309 errAbort("bad input to longSeqTm"); 00310 end = &s[start + len]; 00311 /* Length <= 0 is nonsensical. */ 00312 for (p = &s[start]; p < end; p++) { 00313 if ('G' == *p || 'g' == *p || 'C' == *p || 'c' == *p) 00314 GC_count++; 00315 } 00316 00317 return 00318 81.5 00319 + (16.6 * log10(salt_conc / 1000.0)) 00320 + (41.0 * (((double) GC_count) / len)) 00321 - (600.0 / len); 00322 00323 }
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| double oligoDg | ( | char * | dna | ) |
Definition at line 246 of file oligoTm.c.
References cloneString(), errAbort(), freeMem(), and STATE.
00251 { 00252 register int dg = 0; 00253 register char c; 00254 char *dupe = cloneString(dna); 00255 char *s = dupe; 00256 00257 /* Use a finite-state machine (DFA) to calculate dg s. */ 00258 c = *s; s++; 00259 if (c == 'A') goto A_STATE; 00260 else if (c == 'G') goto G_STATE; 00261 else if (c == 'T') goto T_STATE; 00262 else if (c == 'C') goto C_STATE; 00263 else if (c == 'N') goto N_STATE; 00264 else goto ERROR; 00265 STATE(A); 00266 STATE(T); 00267 STATE(G); 00268 STATE(C); 00269 STATE(N); 00270 00271 DONE: /* dg is now computed for the given sequence. */ 00272 freeMem(dupe); 00273 return dg / 1000.0; 00274 00275 ERROR: 00276 freeMem(dupe); 00277 errAbort("Not a valid oligo in oligoDg."); 00278 return 0; 00279 }
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| double oligoTm | ( | char * | dna, | |
| double | DNA_nM, | |||
| double | K_mM | |||
| ) |
Definition at line 183 of file oligoTm.c.
References cloneString(), ds, errAbort(), freeMem(), STATE, and touppers().
Referenced by seqTm().
00190 { 00191 register int dh = 0, ds = 108; 00192 register char c; 00193 char *dupe = cloneString(dna); 00194 char *s = dupe; 00195 double delta_H, delta_S; 00196 00197 touppers(s); 00198 /* Use a finite-state machine (DFA) to calucluate dh and ds for s. */ 00199 c = *s; s++; 00200 if (c == 'A') goto A_STATE; 00201 else if (c == 'G') goto G_STATE; 00202 else if (c == 'T') goto T_STATE; 00203 else if (c == 'C') goto C_STATE; 00204 else if (c == 'N') goto N_STATE; 00205 else goto ERROR; 00206 STATE(A); 00207 STATE(T); 00208 STATE(G); 00209 STATE(C); 00210 STATE(N); 00211 00212 DONE: /* dh and ds are now computed for the given sequence. */ 00213 delta_H = dh * -100.0; /* 00214 * Nearest-neighbor thermodynamic values for dh 00215 * are given in 100 cal/mol of interaction. 00216 */ 00217 delta_S = ds * -0.1; /* 00218 * Nearest-neighbor thermodynamic values for ds 00219 * are in in .1 cal/K per mol of interaction. 00220 */ 00221 00222 /* 00223 * See Rychlik, Spencer, Roads, Nucleic Acids Research, vol 18, no 21, 00224 * page 6410, eqn (ii). 00225 */ 00226 freeMem(dupe); 00227 return delta_H / (delta_S + 1.987 * log(DNA_nM/4000000000.0)) 00228 - 273.15 + 16.6 * log10(K_mM/1000.0); 00229 00230 ERROR: /* 00231 * length of s was less than 2 or there was an illegal character in 00232 * s. 00233 */ 00234 freeMem(dupe); 00235 errAbort("Not a valid oligo in oligoTm."); 00236 return 0; 00237 }
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| double seqTm | ( | char * | seq, | |
| double | dna_conc, | |||
| double | salt_conc | |||
| ) |
1.5.2
