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  1. Jalview
  2. JAL-157

calculate melting temp of region

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Feature Request
    • Labels:
      None
    • Mantis ID:
      11678

      Description

      highlight a string of bases and calculate the Tm. source from primer3:


      double oligoTm(char *dna, double DNA_nM = 50, double K_mM = 50)
      {
         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.
                                    */
          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);
          /*
           * See Rychlik, Spencer, Roads, Nucleic Acids Research, vol 18, no 21,
           * page 6410, eqn (ii).
           */
          return delta_H / (delta_S + 1.987 * log(DNA_nM/4000000000.0))
              - 273.15 + 16.6 * log10(K_mM/1000.0);
      }

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              Assignee:
              Unassigned Unassigned
              Reporter:
              amwaterhouse Andrew Waterhouse
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                Dates

                Created:
                Updated: