C++ DNA translation problem

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I am trying to make a program that can take Template DNA and show the amino acid sequence that is formed after transcription and translation
It works, but only for 3 bases. I would like it to work for as many bases as possible.
This is what I have:

What I have tried:

#include <iostream>
#include 
#include <string>

using namespace std;

typedef std::map<std::string, std::string> TStrStrMap;
typedef std::pair<std::string, std::string> dnaTemplatePair;

int main(int argc, char *argv[])
{
	TStrStrMap oMap;

	oMap.insert(dnaTemplatePair("TTT", "Phe"));
	oMap.insert(dnaTemplatePair("TTC", "Phe"));
	oMap.insert(dnaTemplatePair("TTA", "Leu"));
	oMap.insert(dnaTemplatePair("TTG", "Leu"));
	oMap.insert(dnaTemplatePair("TCT", "Ser"));
	oMap.insert(dnaTemplatePair("TCC", "Ser"));
	oMap.insert(dnaTemplatePair("TCA", "Ser"));
	oMap.insert(dnaTemplatePair("TCG", "Ser"));
	oMap.insert(dnaTemplatePair("TAT", "Tyr"));
	oMap.insert(dnaTemplatePair("TAC", "Tyr"));
	oMap.insert(dnaTemplatePair("TAA", "STOP"));
	oMap.insert(dnaTemplatePair("TAG", "STOP"));
	oMap.insert(dnaTemplatePair("TGT", "Cys"));
	oMap.insert(dnaTemplatePair("TGC", "Cys"));
	oMap.insert(dnaTemplatePair("TGA", "STOP"));
	oMap.insert(dnaTemplatePair("TGG", "Trp"));
	oMap.insert(dnaTemplatePair("CTT", "Leu"));
	oMap.insert(dnaTemplatePair("CTC", "Leu"));
	oMap.insert(dnaTemplatePair("CTA", "Leu"));
	oMap.insert(dnaTemplatePair("CTG", "Leu"));
	oMap.insert(dnaTemplatePair("CCT", "Pro"));
	oMap.insert(dnaTemplatePair("CCC", "Pro"));
	oMap.insert(dnaTemplatePair("CCA", "Pro"));
	oMap.insert(dnaTemplatePair("CCG", "Pro"));
	oMap.insert(dnaTemplatePair("CAT", "His"));
	oMap.insert(dnaTemplatePair("CAC", "His"));
	oMap.insert(dnaTemplatePair("CAA", "Gln"));
	oMap.insert(dnaTemplatePair("CAG", "Gln"));
	oMap.insert(dnaTemplatePair("CGU", "Arg"));
	oMap.insert(dnaTemplatePair("CGC", "Arg"));
	oMap.insert(dnaTemplatePair("CGA", "Arg"));
	oMap.insert(dnaTemplatePair("CGG", "Arg"));
	oMap.insert(dnaTemplatePair("ATT", "Ile"));
	oMap.insert(dnaTemplatePair("ATC", "Ile"));
	oMap.insert(dnaTemplatePair("ATA", "Ile"));
	oMap.insert(dnaTemplatePair("ATG", "Met"));
	oMap.insert(dnaTemplatePair("ACT", "Thr"));
	oMap.insert(dnaTemplatePair("ACC", "Thr"));
	oMap.insert(dnaTemplatePair("ACA", "Thr"));
	oMap.insert(dnaTemplatePair("ACG", "Thr"));
	oMap.insert(dnaTemplatePair("AAT", "Asn"));
	oMap.insert(dnaTemplatePair("AAC", "Asn"));
	oMap.insert(dnaTemplatePair("AAA", "Lys"));
	oMap.insert(dnaTemplatePair("AAG", "Lys"));
	oMap.insert(dnaTemplatePair("AGT", "Ser"));
	oMap.insert(dnaTemplatePair("AGC", "Ser"));
	oMap.insert(dnaTemplatePair("AGA", "Arg"));
	oMap.insert(dnaTemplatePair("AGG", "Arg"));
	oMap.insert(dnaTemplatePair("GTT", "Val"));
	oMap.insert(dnaTemplatePair("GTC", "Val"));
	oMap.insert(dnaTemplatePair("GTA", "Val"));
	oMap.insert(dnaTemplatePair("GTG", "Val"));
	oMap.insert(dnaTemplatePair("GCT", "Ala"));
	oMap.insert(dnaTemplatePair("GCC", "Ala"));
	oMap.insert(dnaTemplatePair("GCA", "Ala"));
	oMap.insert(dnaTemplatePair("GCG", "Ala"));
	oMap.insert(dnaTemplatePair("GAT", "Asp"));
	oMap.insert(dnaTemplatePair("GAC", "Asp"));
	oMap.insert(dnaTemplatePair("GAA", "Glu"));
	oMap.insert(dnaTemplatePair("GAG", "Glu"));
	oMap.insert(dnaTemplatePair("GGT", "Gly"));
	oMap.insert(dnaTemplatePair("GGC", "Gly"));
	oMap.insert(dnaTemplatePair("GGA", "Gly"));
	oMap.insert(dnaTemplatePair("GGG", "Gly"));
	std::string dnaTemplate;
	std:: cout << "Enter DNA Template: " << std::endl;;
	std:: cin >> dnaTemplate;

	std::string strValue = oMap[dnaTemplate];
	if(strValue!="")
	{
			std::cout << "The Amino Acid Sequence will be: " << strValue << endl;
	}
	else
	{
		TStrStrMap::iterator p;
					bool bFound=false;

			for(p = oMap.begin(); p!=oMap.end(); ++p)
			{
					std::string strKey;
					strValue = dnaTemplate;
					strKey= p->second;
					if( strValue == strKey)
					{

							std::cout << "The Amino Acid Sequence will be: " << p->first << std::endl;
							bFound = true;
					}
			}

			if(!bFound)
			{
					std::cout << "Look at your DNA Template again, and try again." << std::endl;
			}
	}
	return 0;

}

Posted 16-Nov-17 8:58am

Member 13525452

Updated 22-Nov-17 22:11pm

jeron1

v2

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Comments

phil.o 16-Nov-17 16:49pm

You have a map which associates bases-sequences with corresponding amino-acids. You just have to qualify your map with larger bases-sequences.
I suspect it's more a genetic-engineering problem than a coding problem.

Member 13525452 16-Nov-17 18:20pm

How? DNA is randomized and comes in base pairs. Doing every single combination a DNA template could have and putting that into the map would take forever.

phil.o 16-Nov-17 18:31pm

I understand that. But then I do not understand your statement saying you would like it to work with as many bases as possible. Are you talking about the number of bases in the map's keys? What is the question, exactly? You can find lots of code samples which will allow you to find all possible sequences (combinations) of bases of a certain length, but then, you will have somehow to link them to an amino-acid, or to a STOP codon.
Or maybe you simply mean that DNA template can be larger than 3, and you want to split it into 3-bases chunks?
Please clarify.

Member 13525452 21-Nov-17 16:25pm

I just commented below and explained it but to answer the second question. Yes, the input can be larger than 3 and I want it split into 3-bases "chunks."

Bernhard Hiller 17-Nov-17 4:39am

Where is your problem? You just need to iterate thru the input data in junks of 3 bases, find the amino acid for the triplet, take the next triplet, etc.
Only later on you'll think of start and stop codons, and even more complicated cases of sequences around a start codon, splicing, ...

Member 13525452 21-Nov-17 16:23pm

So just to clarify on everything I am going to give an example. If I were to Input ATGTTTGCGTGT, then I want to output a protein sequence. So that sequence would be Met-Phe-Ala-Cys. My program can only accept an input of 3 bases so only ATG, for example, and then it would output Met.

4 solutions

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Mikhail Semenov · Answer 1 · 2017-11-19T03:48:00

Solution 2

You should do something like that:

int n = dnaTemplate.size()-2;
for (int i = 0; i < n; i+=3)
{
   std::string triplet = s.substr(i, 3);
   std::string aminoacid = oMap[triplet];
   ...
}

Posted 19-Nov-17 3:48am

Mikhail Semenov

Comments

Member 13525452 21-Nov-17 16:23pm

Where would I place this?

Mikhail Semenov 21-Nov-17 17:40pm

After you get your template.Instead of ... you put the printing of your amino acid and extra processing if you wish.

Member 13525452 22-Nov-17 15:25pm

Can you be a little more specific. So immediately after if(strValue!="") ?

KarstenK · Answer 2 · 2017-11-17T00:10:00

Solution 1

You need to find and get some database (internet, collegues or schools) and than write some code to work with it. This is a piece of cake.

Posted 17-Nov-17 0:10am

KarstenK

Mikhail Semenov · Answer 3 · 2017-11-22T09:36:00

Solution 3

No, immediately after

std:: cin >> dnaTemplate;

The line

std::string strValue = oMap[dnaTemplate];

is incorrect: you are trying to use the whole string as an index in a map. You should use one triplet at a time.

Posted 22-Nov-17 9:36am

Mikhail Semenov

Comments

Member 13525452 22-Nov-17 15:57pm

so what is s.substr it is not being recognized.

Mikhail Semenov · Answer 4 · 2017-11-22T22:11:00

Solution 4

Sorry, my nmistake:

int n = dnaTemplate.size()-2;
for (int i = 0; i < n; i+=3)
{
   std::string triplet = dnaTemplate.substr(i, 3);
   std::string aminoacid = oMap[triplet];
   ...
}

Posted 22-Nov-17 22:11pm

Mikhail Semenov

Comments

Mikomike123453 27-Nov-17 16:08pm

Hey, I made a new account. Would it be like this?

#include <iostream>
#include
#include <string>

using namespace std;

typedef std::map<std::string, std::string> TStrStrMap;
typedef std::pair<std::string, std::string> dnaTemplatePair;

int main(int argc, char *argv[])
{
TStrStrMap oMap;

oMap.insert(dnaTemplatePair("TTT", "Phe"));
oMap.insert(dnaTemplatePair("TTC", "Phe"));
oMap.insert(dnaTemplatePair("TTA", "Leu"));
oMap.insert(dnaTemplatePair("TTG", "Leu"));
oMap.insert(dnaTemplatePair("TCT", "Ser"));
oMap.insert(dnaTemplatePair("TCC", "Ser"));
oMap.insert(dnaTemplatePair("TCA", "Ser"));
oMap.insert(dnaTemplatePair("TCG", "Ser"));
oMap.insert(dnaTemplatePair("TAT", "Tyr"));
oMap.insert(dnaTemplatePair("TAC", "Tyr"));
oMap.insert(dnaTemplatePair("TAA", "STOP"));
oMap.insert(dnaTemplatePair("TAG", "STOP"));
oMap.insert(dnaTemplatePair("TGT", "Cys"));
oMap.insert(dnaTemplatePair("TGC", "Cys"));
oMap.insert(dnaTemplatePair("TGA", "STOP"));
oMap.insert(dnaTemplatePair("TGG", "Trp"));
oMap.insert(dnaTemplatePair("CTT", "Leu"));
oMap.insert(dnaTemplatePair("CTC", "Leu"));
oMap.insert(dnaTemplatePair("CTA", "Leu"));
oMap.insert(dnaTemplatePair("CTG", "Leu"));
oMap.insert(dnaTemplatePair("CCT", "Pro"));
oMap.insert(dnaTemplatePair("CCC", "Pro"));
oMap.insert(dnaTemplatePair("CCA", "Pro"));
oMap.insert(dnaTemplatePair("CCG", "Pro"));
oMap.insert(dnaTemplatePair("CAT", "His"));
oMap.insert(dnaTemplatePair("CAC", "His"));
oMap.insert(dnaTemplatePair("CAA", "Gln"));
oMap.insert(dnaTemplatePair("CAG", "Gln"));
oMap.insert(dnaTemplatePair("CGU", "Arg"));
oMap.insert(dnaTemplatePair("CGC", "Arg"));
oMap.insert(dnaTemplatePair("CGA", "Arg"));
oMap.insert(dnaTemplatePair("CGG", "Arg"));
oMap.insert(dnaTemplatePair("ATT", "Ile"));
oMap.insert(dnaTemplatePair("ATC", "Ile"));
oMap.insert(dnaTemplatePair("ATA", "Ile"));
oMap.insert(dnaTemplatePair("ATG", "Met"));
oMap.insert(dnaTemplatePair("ACT", "Thr"));
oMap.insert(dnaTemplatePair("ACC", "Thr"));
oMap.insert(dnaTemplatePair("ACA", "Thr"));
oMap.insert(dnaTemplatePair("ACG", "Thr"));
oMap.insert(dnaTemplatePair("AAT", "Asn"));
oMap.insert(dnaTemplatePair("AAC", "Asn"));
oMap.insert(dnaTemplatePair("AAA", "Lys"));
oMap.insert(dnaTemplatePair("AAG", "Lys"));
oMap.insert(dnaTemplatePair("AGT", "Ser"));
oMap.insert(dnaTemplatePair("AGC", "Ser"));
oMap.insert(dnaTemplatePair("AGA", "Arg"));
oMap.insert(dnaTemplatePair("AGG", "Arg"));
oMap.insert(dnaTemplatePair("GTT", "Val"));
oMap.insert(dnaTemplatePair("GTC", "Val"));
oMap.insert(dnaTemplatePair("GTA", "Val"));
oMap.insert(dnaTemplatePair("GTG", "Val"));
oMap.insert(dnaTemplatePair("GCT", "Ala"));
oMap.insert(dnaTemplatePair("GCC", "Ala"));
oMap.insert(dnaTemplatePair("GCA", "Ala"));
oMap.insert(dnaTemplatePair("GCG", "Ala"));
oMap.insert(dnaTemplatePair("GAT", "Asp"));
oMap.insert(dnaTemplatePair("GAC", "Asp"));
oMap.insert(dnaTemplatePair("GAA", "Glu"));
oMap.insert(dnaTemplatePair("GAG", "Glu"));
oMap.insert(dnaTemplatePair("GGT", "Gly"));
oMap.insert(dnaTemplatePair("GGC", "Gly"));
oMap.insert(dnaTemplatePair("GGA", "Gly"));
oMap.insert(dnaTemplatePair("GGG", "Gly"));
std::string dnaTemplate;
std:: cout << "Enter DNA Template: " << std::endl;;
std:: cin >> dnaTemplate;
int n = dnaTemplate.size()-2;
for (int i = 0; i < n; i+=3)
{
std::string triplet = dnaTemplate.substr(i, 3);
std::string strValue = oMap[triplet];
if(strValue!="")
}
{
std::cout << "The Amino Acid Sequence will be: " << strValue << endl;
}
else
{
TStrStrMap::iterator p;
bool bFound=false;

for(p = oMap.begin(); p!=oMap.end(); ++p)
{
std::string strKey;
strValue = dnaTemplate;
strKey= p->second;
if( strValue == strKey)
{

std::cout << "The Amino Acid Sequ