inc/oligoTm.h File Reference

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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)

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Function Documentation

double longSeqTm	(	char *	s,
		int	start,
		int	len,
		double	salt_conc
	)

Definition at line 282 of file oligoTm.c.

References errAbort().

Referenced by seqTm().

                                            :1390 (1962) as presented in
 * Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11.46 (1989, CSHL
 * Press).
 *
 * Tm = 81.5 + 16.6(log10([Na+])) + .41*(%GC) - 600/length
 *
 * Where [Na+] is the molar sodium concentration, (%GC) is the percent of Gs
 * and Cs in the sequence, and length is the length of the sequence.
 *
 * A similar formula is used by the prime primer selection program in GCG
 * (http://www.gcg.com), which instead uses 675.0 / length in the last term
 * (after F. Baldino, Jr, M.-F. Chesselet, and M.E.  Lewis, Methods in
 * Enzymology 168:766 (1989) eqn (1) on page 766 without the mismatch and
 * formamide terms).  The formulas here and in Baldino et al. assume Na+ rather
 * than K+.  According to J.G. Wetmur, Critical Reviews in BioChem. and
 * Mol. Bio. 26:227 (1991) 50 mM K+ should be equivalent in these formulae to .2
 * M Na+.
 *
 * This function takes salt_conc to be the millimolar (mM) concentration,
 * since mM is the usual units in PCR applications.  */
{
  int GC_count = 0;
  char *p, *end;

  if(start + len > strlen(s) || start < 0 || len <= 0) 
        errAbort("bad input to longSeqTm");
  end = &s[start + len];
  /* Length <= 0 is nonsensical. */
  for (p = &s[start]; p < end; p++) {
    if ('G' == *p || 'g' == *p || 'C' == *p || 'c' == *p)
      GC_count++;
  }

  return
    81.5
    + (16.6 * log10(salt_conc / 1000.0))
    + (41.0 * (((double) GC_count) / len))
    - (600.0 / len);

}

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double oligoDg

(

char *

dna

)

Definition at line 246 of file oligoTm.c.

References cloneString(), errAbort(), freeMem(), and STATE.

{
    register int dg = 0;
    register char c;
    char *dupe = cloneString(dna);
    char *s = dupe;

    /* Use a finite-state machine (DFA) to calculate dg s. */
    c = *s; s++;
    if (c == 'A') goto A_STATE;
    else if (c == 'G') goto G_STATE;
    else if (c == 'T') goto T_STATE;
    else if (c == 'C') goto C_STATE;
    else if (c == 'N') goto N_STATE;
    else goto ERROR;
    STATE(A);
    STATE(T);
    STATE(G);
    STATE(C);
    STATE(N);

    DONE:  /* dg is now computed for the given sequence. */
    freeMem(dupe);
    return dg / 1000.0;

    ERROR:
    freeMem(dupe);
    errAbort("Not a valid oligo in oligoDg.");
    return 0;
}

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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().

{
    register int dh = 0, ds = 108;
    register char c;
    char *dupe = cloneString(dna);
    char *s = dupe;
    double delta_H, delta_S;

    touppers(s);
    /* Use a finite-state machine (DFA) to calucluate dh and ds for s. */
    c = *s; s++;
    if (c == 'A') goto A_STATE;
    else if (c == 'G') goto G_STATE;
    else if (c == 'T') goto T_STATE;
    else if (c == 'C') goto C_STATE;
    else if (c == 'N') goto N_STATE;
    else goto ERROR;
    STATE(A);
    STATE(T);
    STATE(G);
    STATE(C);
    STATE(N);

    DONE:  /* dh and ds are now computed for the given sequence. */
    delta_H = dh * -100.0;  /* 
                             * Nearest-neighbor thermodynamic values for dh
                             * are given in 100 cal/mol of interaction.
                             */
    delta_S = ds * -0.1;     /*
                              * Nearest-neighbor thermodynamic values for ds
                              * are in in .1 cal/K per mol of interaction.
                              */

    /* 
     * See Rychlik, Spencer, Roads, Nucleic Acids Research, vol 18, no 21,
     * page 6410, eqn (ii).
     */
    freeMem(dupe);
    return delta_H / (delta_S + 1.987 * log(DNA_nM/4000000000.0))
        - 273.15 + 16.6 * log10(K_mM/1000.0);

    ERROR:  /* 
          * length of s was less than 2 or there was an illegal character in
          * s.
          */
    freeMem(dupe);
    errAbort("Not a valid oligo in oligoTm.");
    return 0;
}

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double seqTm	(	char *	seq,
		double	dna_conc,
		double	salt_conc
	)

Definition at line 325 of file oligoTm.c.

References longSeqTm(), and oligoTm().

{
  int len = strlen(seq);
  return (len > 36)
    ? longSeqTm(seq, 0, len, salt_conc) : oligoTm(seq, dna_conc, salt_conc);
}

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