c++计算DNA探针的熔解温度

DNA探针的熔解温度（Tm）是指DNA双链在解离过程中的温度，可以用来估计DNA探针与靶序列的结合强度。

DNA探针富集实验中使用的盐浓度通常是在高盐条件下进行的，以帮助DNA与探针结合并提高富集效率。一般来说，盐浓度在0.5 M到1 M之间是常见的范围，但具体的盐浓度会根据实验的具体条件和目的而有所不同。例如，常用的盐包括NaCl和NaI。

DNA探针富集实验中常用的二价阳离子是Mg^2+。Mg^2+离子在DNA结合和酶活性中起着重要作用，因此通常需要在实验中添加适量的Mg^2+。一般来说，Mg^2+的浓度可以在0.5 mM到10 mM范围内变化，具体的浓度取决于实验条件、所用的DNA探针和靶序列的特性以及所需的结合强度等因素。

//
//  main.cpp
//  test3
//
//  Created by  zhengxueming on 2024/4/22.
//

#include <iostream>
#include <math.h>
#include <string.h>

#define BAIT_ERROR -1

using namespace std;

double divalentToMonovalent(double divalent, double dntp) {
   if(divalent==0) dntp=0;
   if(divalent<0 || dntp<0) return BAIT_ERROR;
   if(divalent<dntp)
     /* According to theory, melting temperature does not depend on
    divalent cations */
     divalent=dntp;
   return 120*(sqrt(divalent-dntp));
}


/*
const string seq: The bait DNA sequence
 
double salt_conc: Concentration of divalent cations (millimolar).
一般来说，盐浓度在0.5 M到1 M之间是常见的范围常用的盐包括NaCl和NaI
 
double dna_conc: DNA concentration (nanomolar).
double divalent_conc: Concentration of divalent cations (millimolar)
double dntp_conc: Concentration of dNTPs (millimolar)

*/


double
calBaitTm(const string seq, double salt_conc=50,
            double divalent_conc=0.5, double dntp_conc=0)
{
    int GC_count = 0;
    //const char *p, *end;
    if (divalentToMonovalent(divalent_conc, dntp_conc) == BAIT_ERROR)
        return BAIT_ERROR;
  
    salt_conc = salt_conc + divalentToMonovalent(divalent_conc, dntp_conc);
    
    //std::cout << salt_conc << std::endl;
 
    /* Length <= 0 is nonsensical. */
    for (auto base: seq) {
        if (base == 'G' || base == 'C')
          GC_count++;
     }
    
    int64_t len = seq.size();
    
    //std::cout << len << std::endl;
    
    return
        81.5
        + (16.6 * log10(salt_conc / 1000.0))
        + (41.0 * (((double) GC_count) / len))
        - (600.0 / len);
}


int main(int argc, const char * argv[]) {
    // insert code here...
    
    const string normal_bait = "ACAAAGAAATCTCATATTGCTAATGAAGTTGAAGAAAATGACAGCATCTTTGTAAAGCTTCTTAAGATATCAGGAATTATTCTTAAAACGGGAGAGAGTCAGAATCAACTAGGTAATATT";
    
    const string high_gc_bait = "GCCCGGGGCGCGCGCGCGCGCGCGCAGTTGAAGAAAATGCCCGGGGCGCGCGCGCGCGCGCGCATGCCCGGGGCGCGCGCGCGCGCGCGCATC";

    const string high_at_bait = "TTGAATAAAATATTGAATAAAATATTGAATAAAATATTGAATAAAATATTGAATAAAATATTGAATAAAATATTGAATAAAATTTGAATAAAATA";
    
    std::cout << "normal_bait tm: " << calBaitTm(normal_bait) << std::endl;
    std::cout << "high_gc_bait tm: " << calBaitTm(high_gc_bait)<< std::endl;
    
    std::cout << "high_at_bait tm: " << calBaitTm(high_at_bait)<< std::endl;

    return 0;
}