Geek Answers Handbook

How to complete obtaining substrings of a genome encoding a given amino acid sequence

The problem of coding peptides is to search for substrings of the genome encoding a given amino acid sequence.

The genetic code describes the translation of 3-mer RNA (codon) into one of 20 different amino acids. The first three circles moving from the inside are the 1st, 2nd and 3rd nucleotides of this codon. The 4th, 5th and 6th circles define the translated amino acid in three ways: the full name of the amino acids, its three-letter abbreviation, and the one-letter abbreviation. Three of the 64 complete RNA codons are stop codons that stop translation and implicitly add the 21st stop symbol to the amino acid alphabet.

enter image description here

The challenge is to have

: - .

: ( ).

Sample Input:
     ATGGCCATGGCCCCCAGAACTGAGATCAATAGTACCCGTATTAACGGGTGA
     MA

Sample Output:
     ATGGCC
     GGCCAT
     ATGGCC

, ATGGCC MA, GGCCAT CCGGTA , ATGGCC (CCGGTA.reverse)

C-G, G-C, T-A A-T

, ,

using System;
using System.Collections.Generic;
using System.Text;
using System.Text.RegularExpressions;
using System.Linq;
using System.IO;
using System.Collections;


class Program
{
    private static string[] CODONS = { 
                "TTT", "TTC", "TTA", "TTG", "TCT",
                "TCC", "TCA", "TCG", "TAT", "TAC", "TGT", "TGC", "TGG", "CTT",
                "CTC", "CTA", "CTG", "CCT", "CCC", "CCA", "CCG", "CAT", "CAC",
                "CAA", "CAG", "CGT", "CGC", "CGA", "CGG", "ATT", "ATC", "ATA",
                "ATG", "ACT", "ACC", "ACA", "ACG", "AAT", "AAC", "AAA", "AAG",
                "AGT", "AGC", "AGA", "AGG", "GTT", "GTC", "GTA", "GTG", "GCT",
                "GCC", "GCA", "GCG", "GAT", "GAC", "GAA", "GAG", "GGT", "GGC",
                "GGA", "GGG", };

    private static  string[] AMINOS_PER_CODON = { 
            "F", "F", "L", "L", "S", "S",
            "S", "S", "Y", "Y", "C", "C", "W", "L", "L", "L", "L", "P", "P",
            "P", "P", "H", "H", "Q", "Q", "R", "R", "R", "R", "I", "I", "I",
            "M", "T", "T", "T", "T", "N", "N", "K", "K", "S", "S", "R", "R",
            "V", "V", "V", "V", "A", "A", "A", "A", "D", "D", "E", "E", "G",
            "G", "G", "G", };

    private static  string[] AMINO_ABBREVIATIONS = {
            "F", "L", "I", "M", "V",
            "S", "P", "T", "A", "Y", "H", "Q", "N", "K", "D", "E", "C", "W",
            "R", "G" };

    private static string[] FULL_NAMES = { 
            "phenylalanine", "leucine",
            "isoleucine", "methionine", "valine", "serine", "proline",
            "threonine", "alanine", "tyrosine", "histidine", "glutamine",
            "asparagine", "lysine", "aspartic acid", "glutamic acid",
            "cysteine", "tryptophan", "arginine", "glycine" };

  static void Main()
  {
    //then input is DNA
    string dna = "TTCGAATCCGTATTGCTTTGGTTGGTTGAGAGAGCGACCTACATTGCTAGTCAGAATAGGTGATTCACACAAAGCTTAGCACCTGGGCAGCACCCCGTGATGTAAACCTATGGGAACTAAGGGAGTCCTGCGGTTTTAGCCAGCAAGCGAGCCGGCAGGAACACTCATACCATCGGACGCGTTTGACGCCTCCCCGGAAAGGAAGTATTTGAGCCTCATTATTACGTATTGCCCGTTAGTCGACAAATCAAGCCCTCGTACGCAGCTTATTCGTACGACGTGGAGGCGTTCCCACGGGCCTAACACGATTGGAACACCACCATAGTAGTGTGGTTCAAATACCTCCTTTGGAGATCTAGAGCTTCACTCTGATTCTAGAGGCAACTTTACAATCGCTCTACGAAATTGTATGGACATCATCAACCGGATATTCTGGGGCGGTAGAATTTCTTTTGTTCGAATCGCTCTAGGCCAGGATCAAATTAATTGAATTGCGGACTCAAGGATCGCGATAGCCGACACATCGGACGCTGTAGAAAGCCAGTCTCTGGATTTAATCCACCCTCTATGTTTGACAAAGCACTAAAACGGGATAGTTTCGGGTGGTATAAGTTTCCCAAGACGATTGCATCGCAATTCATCAACAACCATGAACTTACTGTTTTAGTACTTCCACACACCTTGTTAAATTACGCCTTTACTTCATGTTGCGGTGTGTGTTAGATAGTGTGCAGCTACAAGTCTACCGCCATCGCAGCTCGGGATACCGGCAGATGAGATGGTCCTGAGCTCGTACCGGACTCAAACTTTTTCCTTTACTACCTAGGAATCGCCCATGCGAATTTGTCGGACACACACCATTACATTAACGTCACAACAGCTACTGTTAGAATTTTGCTCTTGCAAATCCTGGAAAGAGTTAAAAAAACTCTTCCGCGCGCCAATAGGGTAAATAATAGATAGCCAGACGGCTGTAAGAGGTGATGACATTTGCAACAATCATGCTGTCGCATCTTCCGCAAGTTCATGTCGCGCCTAGGCAATGGATCTGCGAATGGGGGCCACGGGGTATGAACTACGGAATTCTAAGAAAGTTGCCATCCAGAGTTAAGGGTTTGAGGCTAGTTGCATCGCTGGTAACGAACTACCTCATTACTTGGACGCGCAGTGTGACTTCACTCCTGTATAGCGATGATGCCAAGCAGGAATTAGCAAATCTGAAGAGCGTTTCCAAACTGGCCACTTGGACTGACACCTATCGCGGGGGATTTCAGCGCGTGTCGCTCTCACATGAGAGCTGCCGTCAGGAGCGGTAGAGTTTAGAGAGGAATGCGACAAACTCCCTATTCACCTCTCTGGTGATGTAAGGATATTTACGCTTAGTTCTATGCCAGGCTTAGGGCCTCTCGGAACTTTGGTGAGTCCTTATTAATTGATGCTACCTCTCCCTTACCTTCGCCCCAAGTCACGTAGAAGTACTCAATCCTGCTACATGATAATCAAATATTTCCAACGTTGGGAAATCGGTGACATCACATACTAGTTAAGAAACCACTGTCAGTGAACTTATATCCGGGGGAGAAAATCTACTAACTTACATACGCTGTGCGAGCAGTTTTCATTATAAGAAAATATACTCCCGAGGTACCGCATCAAGCACGACATTCCCGGAGAGCATAACATTTCGGTGCACCTGCTTTTGTGCGCTTGCTTGCGGTTATTTATAAACTACGCACAAGGCGCAAACCGCAGTGCGCATGTTTTCTCCGCCTGGCTAGAACTCGACATTCTCGTCAACGCCAATCTATGTGAGAGGATTTAGACCTCTGTGAAAACGAGTCCCTCTATAGAATAAATACCCAGATGCCAATGGGGGTTCTATCCGATGGCAGTGCATGGAGTGGTGGCTCCAGATTAAGGATGAGGAGAGGTAAAGATAACAGTTCGGTCGCCACGACGCGTTGCCAATCGAAATATCAGTACTAAAAGGCCCACCGCTCCGCTTTAGTCCGACTTTACATCCTGTGGAAATTGTCGAACGGAGGCTACATCGGGCTATATGAGTGTGAAAACCTATACTTCTCGCGTCGTTACTCAGTGCCGGTCTCCTGTTTCCCCCAGTCTTACGTACCCTTATTGATATTTGCTTCACGTTGAAACGTCCTAACGCAGCGTAAAGAGGTGTTTGAACCTCATTACTATAAAATCGCGATCGAAGGTAGACTACATACGCAAACGCCGAAACCCTCAGTTGGCCTTGTTGCAAGTATGGAACGTTGTAAAATTTTTCCTAGACGTTGAGCTATCGGTACAAGGTCGTTAGCGTCCTTACCCTTCACTTATATGCCCGACAAAACGCGGGTCCTAGTGCAGTGGTGGGAGCTTGGAATCCCGCAATACAAGGACAACCTGTATCTCGTTCGGCGTTCCGCGATCACTCGATCCCGAACCACTCCAAGCCTGGTTGATCAGCAAAAGCGGAAGGATGGATAAAGGGCTACTGGTTAATGGATGTAAACTTCCAATGATGAAATCCTGGAAACGAGGGATCGGGTTACGGTGGCGAACGGGGTACGGCAACGTGGCTATCTAGAGCCCGACGTTACGACTCATGTACATGCTGCTACGTGGTTGAAGCTGACGTTCAGATGAAGCAGTACTGAGTCCTAGGGCTTACTACTACTCCAATAGGTCTGGCCGGCCAGATACAAAAGTTCGTGGCGGCTCACCCCCTTTCTGGCGGGTGTAGCTTGCTGACCGGTTTGCTCGATAACACAGGCTAGCGAATAGTAATGAGGTTCGAAAACCTCTTTCCAACGACTGAAAGGGTCTACACGAACTATCTACATTTCCCCGCCCATGTCCTTCCGTCTGGTTGCTTCTGGAGATCCTTTCGCATTATACCGCAGCGTAGTGGCTCTGGCATATATGAAAAAATCCTTCTGTGGGTATTTGTGCCATCACTTATTGTTCGTACCGATATGGGATTACAAGTGCGATGTGATAATAAGCGAAGAAGCCAACATGTTACACTGTTCATGCGCTCCGGGTAATGTGCGGGCACCATGCTCAGTTCCCGCTCGCAGTTGTCACTGTCCCTGTTTCGGCACCATAATCAACATTTCCACGGCCACGCTGGTGAATAACCGAGGATACCGAAGTACAGCAAGAATGAGAGCGGGACTCCTCCATCTGCTTGTAATACGCCTTCAAGATAGTCCATAAAACGGTCGGGGTCTTGTTTCGGACTAGCCGCTTTGAAACGGTGCATAGTTGTGTCAAGTGTGGACATTGGCTTTCTATCCTCGTCAGCGATCCTCGGAAAGACTCGGGCAGTCGCCCCGAATCGTAATTAGGTAGTAGTGCGGCTCAAAAACTTCCTTCGACCTAACCGCTATAATGTTCGTAGATATAAATTTCGTTTCAGTATTAACAGGCGCACCGTATATATACGGAATGGTGTCGCCCCATTAGCTGCTCGCCAATATTTATCTAAGACCGCGCGCGTCTAGCGCCTTTAGTAGTTGCACCCGAGTATAGTAATGGGGTTCGAAGACTTCCTTCGCAAGGCTGCCATACTGTATCACAAGTACTGACGGAGCCCCGGAGGAGTGCAGGATACGGCAAAGGAGACCATTACCGGGGCATGAGTCCAAGTTAGCCCGTTAGGTGAAGGACGCTGATACAATAGTGAATCCGTTACTGAAAGGTTTAGAAGACCGGGGGGCTCGCACTAGGTCCAAATATTATGAACCCTACTCCTGCAACTGAATTGGCCGTCCAGGCGATATTTAAAAGGGGTTACTAGCAGGTTCATCGGAGCCCGTACTCCTTCCGGGCATAGTCGTTCGACGGGTAGAAATTCATCCAGTCGTGCCGGATACCCCGAGAATACCCCTATTTTTTGATCCTTCACCATCATCGTCCGCGGACTCATCTAAGTACCTCAGACCGAAACTGTTATCGTAGCGAAGAGCGAACTCGAATGACATCGCTTGTCCAACAGGGAAAATATGTAAAGTATATGCAGATTATTATAGGAAGATCACAAACTCCATCGCGCCTAGGCCAAAGACTTGCCAGAACAACATCTCTTCCAGAGCAAGGAAGTGTTTGAACCTCACTATTATCGAGAGAAGTCCCATGAATTTATAATAGTGAGGCTCAAAAACTTCCTTCATCGTCGGGCGCTGGGGCGAGCTAGGCTTCCCTAGCCGTCATTACTGTACCCACGCCAAATATTATCGAGTATGACTACGAAGCCTTCACAAGGGGCTGCAGTAACAGACTAACTCACGCACACCGCAACTACTATCCTAAATTGAGTAAGAAAACCCTCGACTATAGCCCTTGAATTAAATTCGCTATTTAAGGAAGACCGCGCTTCCGCTCGCCCGCGTATAGTTTACCAGTCCCAAGAAACATGTGTGGCCAGCCTACCTGAAGAGCTGTGTAAAGATAGATTCTGACATCCTCAAAAAGAAGTTTTCGAGCCGCACTACTACGCACGGAGCTCCGTTATTCAAGGCATGTCGAAGTACAGCGTGGTGGCCTCTCCTGTTCTCCACCCCAGCTAAACCCACCTTGTTCGAATTCGCGCAACTGTATATGACATGAACACTTACAGGGGTTAGAAGTTACTGCAACCAAGATAGAGCTCGTCGAAGTAATAGTGCGGTTCAAAAACTTCCTTCAATTGGTCTCATCACTTAAATTTAAGAGCTATTGTGAGTACAGGTACGGATGCGGCTTCAGTGGATCTTCAGCATTCATTCCTTGTAGTAATGGGGTTCGAAGACTTCCTTGCCAGGGTACCAAACAAGTCTTGCGCATCCTCCTCCCTAAGGAGGTATTTGAACCCCACTATTACCCACGATAGAACATGCAGGGTTTGATAGTGGAACACCTTTTAGAATCTGGGGATAAATTCCCAGGACTAATGTATGGCTGTAGTAATGAGGTTCAAAAACCTCCTTTTCAGGTGGATCGCAGGCCGTGCTGCCTCACAAGCTGGGACGCCGTCCACGGTATAGCCGGCGTCGGCAGTTACTGTGAAATAGCGGAAACTCGATCCCAATATATCATCTTACGTTTGGCGCCCAATAGTCGCCCAGTACCCGTTGACAGTTCTTTAACTCGGCTTAGAACTACTAGACAGGTTCAACCGAACCTTGCCCTAGTTCCCACTCCCGTAATTCATTTGGGTTTGCATCTAGAATACTGGAGGGTGCATAGACGAAACGTGTACGTCGGAGAAAACGTAAGAAAATGACCTAGACTCATAGTAGTGAGGTTCGAAGACTTCCTTTCAGTGAAATCGATCCACCACTCGCCGCGAAGAGATAATAGCATAGAGCACAAGTGCGCGAGTAGAGAAAAAGGCTATCCCAACCGGGCACGTCCTTCGTGTTTGGCGTTTACATACGGCACCCCGTTTCTGCACGTTAACCGTCTAGTATCCAACGGTGGATGGCGGACGCTAGACTATAGATATGAGATATCGAGACCTGGAGCTGGGTGTGGCTGCAGCCCGGGTCATTGCGGGCTGTGAATTCAAGGGCATGTAAACAAGCGTATATCGAACAGTGGATGGGCACCTGCAATACTCACGGTAGAGTTAGCTCACAGGATTCACGTTGAGGACTATGAGTCCCTCTTCGCTAGCAGTCTGGGGGGATATGGAGTTTAATAGCTTGACGTAGTAATGGGGCTCAAACACCTCTTTGTGTGAGCACAGCTACTTGCATTAAGAGATTCTAAACAGCGATCATCTCGGCTATTTCGGGCCAGCCTTTTCGGCAGGATGTTATGTAGCATTTCTGGAAGCTTCCCCCTCGAATCTACTAGTGGTGAGAAGATGCCCCACCGATATTACTCTTTAATCTTGAGAAACCTAAAACCGATCTGACCTCAGACGGGCGGCTCCCACCCGAGGATAAACTCGTCAATAATAATGTGGCTCGAACACTTCTTTTCTCACTAGGCTTTTACGACACGCCACATGTATTTAAGCATCTACCTAACTTGTGTCTGCTGATATACAGCGCATTCTACGCCCAACCTACCAATTACTTCAACGTAGTGCGTGGCTAAAATTCAGGGGAGCTTCATCTCTGTCTTAATTTGAAGGTTCTTCCGGGGCGTTTGGGAATCTTCGTGCCTTTTGCGAGGTTAAGGTATCAAAGAAGTTTTCGAACCACATTATTACCGCCTTAAGCACCGGCGCATCCTGCTCGTGACAACTCTACCCTGCCCTGATAAAGGCACTGAACGTTCCAGAGAGTGCATCATTGACACGCGAGCAGGCCACAGTAGCCACAAGACGTATGGGTGATTATAGAATTGGTGGAGGTGTTGTTAACGATCAGGAGGACATTAGTGGGAGTTAGGAAAGACCCTATGTTCTCTCTATCGCGGACTTGTAACTTGACAAGCAAAAGGGTAAGAGAGCTGCACACCGAAGCAGGCCCTTCCTATACCTGTTTTTCCTACGCGTAGAGAGGAATCCAGAAAGGTGATAATTGGCATTCGATGAAAAAACAGTGTGCCACTGACTTAGTTCTATATGTGAAGAGCCTGTTAGCACGTGACGGCGGCCTTGGTATAGAGCCCTTAATGGTCTCCATCGCGTAGTAATGGGGCTCGAAAACCTCCTTACTTGGGATTGCGTGGCCTCCTTGTGAGTCATACACAAGGCTTAGGGCTATGGGGCGATACACTCCTTTTCGCGGCGCATGGGGCGGTGATGCCTACATAGTAGTAGTGACTGCCTTTCTGGGGGGCTATTTGTGGATGACCAACACCTGACCAGCGATGCAATCGCTAGGGGAGGTACACCTCTCATATGTTACAACAATCACCGAATTGTGTTTCGAATTCGAATCAAGTTTGCGGTGTCGACCAGATCTGGTCTTGCTGCCATACCGGGTTCGCCGCCTCCGGTGGATAGAACTGCATCTTAAGACATCTGGACCCAGCGGTAAGTAGCGGGAAGAGTTTAGAGTCATTCGTACAACTACAGGCTAAGGGCTTACTGGGGAGTTGTTGTAGGGCATAAAGATCGCCCCATGACTTTTCGTACTTTCCCCGATAGTTCACTCGCAGCGAGCTGCGGCTGGGCTTCGCCACACGAGTACGGGCAACATTTATCTCCTCTAATCACTGGGCACCGCGCGAGGAAATAGAAAACCCTAATCAGTGCTCATGGGCGCATCTATTGGTCTCCGCATGCACGATGCCGCGGAGTGCTTAGTTGTCCCTGCATAATCTTCGTAGATGTATAAGAGATTACCTATTTATTCGGTTTCGGTTCTAGACGTACCTTGCCGCATGAGTATAGGCTAATGAACTGAGTTGGCGCCAGAGGGAAAGGCATAATAATGCGGCTCGAATACTTCCTTAAGGAAGTATTCGAACCACATTACTAT";


    //The given peptide 
                    string givenPeptide = "KEVFEPHYY";
                    char[] givenPeptideArray = givenPeptide.ToCharArray() ;
                    string codon="";
                    string auxCodon="";
                    string convertedCodon = "";
                    string clean = "";
                    int pivot = 0;
                    int foundFlag = 0;
                    string cleanReverse = "";
                    int foundFlagReverse = 0;
                    string convertedCodonReverse = "";



    //so the idea I was working was to loop dna string until getting to 3*givenPeptide.Length 
    //because dna is red 3 by 3... 
    //then get givenPeptide.Length and compare each char of given peptide with encoded 
    //letter of scanned triplet 
    //so for example first givenpeptide is 'M' so I would search for 'ATG'
    //then, if found increment a counter and then search for next 'GCC' etc...
    //however When testing with longer string I do not get complete result
    //I have


                    for (int pos = 0; pos < dna.Length - (3*givenPeptide.Length)   ; pos++) {
                        pivot = pos;
                        for (int codonPos = 0; codonPos < givenPeptide.Length; codonPos++)
                        {
                            codon = dna.Substring(pivot, 3);
                            auxCodon = givenPeptideArray[codonPos].ToString();
                            convertedCodon = codonToAminoAcid(codon);
                            convertedCodonReverse = codonToAminoAcid(DNAComplement(codon));
                            if (auxCodon.Equals(convertedCodon) )
                            {
                                foundFlag++;
                                clean += codon;
                            }
                            else
                            {
                                foundFlag = 0;
                                clean = "";
                            }
                            if (foundFlag == givenPeptide.Length)
                            {
                                Console.WriteLine(clean);
                                foundFlag = 0;
                                clean = "";
                            }
                            //reverse
                            if (auxCodon.Equals(convertedCodonReverse))
                            {
                                foundFlagReverse++;
                                cleanReverse += codon;
                            }
                            else
                            {
                                foundFlagReverse = 0;
                                cleanReverse = "";
                            }
                            if (foundFlagReverse == givenPeptide.Length)
                            {
                                Console.WriteLine(cleanReverse);
                                foundFlagReverse = 0;
                                cleanReverse = "";
                            }
                            pivot+=3;
                        }
                    }
    }//end main

    public static string DNAComplement(string dna)
            {
                char[] array = dna.ToCharArray();
                for (int i = 0; i < array.Length; i++)
                {
                    char let = array[i];
                    if      (let == 'A') array[i] = 'T';
                    else if (let == 'T') array[i] = 'A';
                    else if (let == 'C') array[i] = 'G';
                    else if (let == 'G') array[i] = 'C';
                }

                Array.Reverse(array);
                return new string(array);
            }


    public static string codonToAminoAcid(String codon)
            {

                for (int k = 0; k < CODONS.Length ; k++)
                {
                    if (CODONS[k].Equals (codon))
                    {
                        return AMINOS_PER_CODON[k];
                    }
                }

                // never reach here with valid codon
                return "X";
            }

}//end class


AAGGAAGTATTTGAGCCTCATTATTAC
AAAGAGGTGTTTGAACCTCATTACTAT
AAGGAGGTATTTGAACCCCACTATTAC
AAAGAAGTTTTCGAACCACATTATTAC
AAGGAAGTGTTTGAACCTCACTATTAT
AAAGAAGTTTTCGAGCCGCACTACTAC
AAGGAAGTATTCGAACCACATTACTAT
ATAATAATGCGGCTCGAATACTTCCTT
GTAGTAATGGGGCTCGAAAACCTCCTT
GTAGTAATGAGGTTCAAAAACCTCCTT
GTAGTAATGGGGTTCGAAGACTTCCTT
ATAATAGTGAGGCTCAAAAACTTCCTT
ATAGTAATGGGGTTCGAAGACTTCCTT
GTAGTAGTGCGGCTCAAAAACTTCCTT
ATAGTAATGAGGTTCGAAAACCTCTTT
ATAATAATGTGGCTCGAACACTTCTTT
GTAGTAATGGGGCTCAAACACCTCTTT
ATAGTAGTGAGGTTCGAAGACTTCCTT
GTAATAGTGCGGTTCAAAAACTTCCTT
ATAGTAGTGTGGTTCAAATACCTCCTT

:

AAGGAAGTATTTGAGCCTCATTATTAC
AAAGAGGTGTTTGAACCTCATTACTAT
AAGGAAGTGTTTGAACCTCACTATTAT
AAAGAAGTTTTCGAGCCGCACTACTAC
AAGGAGGTATTTGAACCCCACTATTAC
AAAGAAGTTTTCGAACCACATTATTAC

, , , ...

+4
1

, . , dna. -, , (givenPeptideLength * 3) , . , , , , . .

using System;
using System.Collections.Generic;
using System.Text;
using System.Text.RegularExpressions;
using System.Linq;
using System.IO;
using System.Collections;

namespace DNA
{
    class Program
    {
        private static string[] CODONS = { 
                "TTT", "TTC", "TTA", "TTG", "TCT",
                "TCC", "TCA", "TCG", "TAT", "TAC", "TGT", "TGC", "TGG", "CTT",
                "CTC", "CTA", "CTG", "CCT", "CCC", "CCA", "CCG", "CAT", "CAC",
                "CAA", "CAG", "CGT", "CGC", "CGA", "CGG", "ATT", "ATC", "ATA",
                "ATG", "ACT", "ACC", "ACA", "ACG", "AAT", "AAC", "AAA", "AAG",
                "AGT", "AGC", "AGA", "AGG", "GTT", "GTC", "GTA", "GTG", "GCT",
                "GCC", "GCA", "GCG", "GAT", "GAC", "GAA", "GAG", "GGT", "GGC",
                "GGA", "GGG", };

        private static string[] AMINOS_PER_CODON = { 
            "F", "F", "L", "L", "S", "S",
            "S", "S", "Y", "Y", "C", "C", "W", "L", "L", "L", "L", "P", "P",
            "P", "P", "H", "H", "Q", "Q", "R", "R", "R", "R", "I", "I", "I",
            "M", "T", "T", "T", "T", "N", "N", "K", "K", "S", "S", "R", "R",
            "V", "V", "V", "V", "A", "A", "A", "A", "D", "D", "E", "E", "G",
            "G", "G", "G", };

        private static string[] AMINO_ABBREVIATIONS = {
            "F", "L", "I", "M", "V",
            "S", "P", "T", "A", "Y", "H", "Q", "N", "K", "D", "E", "C", "W",
            "R", "G" };

        private static string[] FULL_NAMES = { 
            "phenylalanine", "leucine",
            "isoleucine", "methionine", "valine", "serine", "proline",
            "threonine", "alanine", "tyrosine", "histidine", "glutamine",
            "asparagine", "lysine", "aspartic acid", "glutamic acid",
            "cysteine", "tryptophan", "arginine", "glycine" };

        public static string DNAComplement(string dna)
        {
            char[] array = dna.ToCharArray();
            for (int i = 0; i < array.Length; i++)
            {
                char let = array[i];
                if (let == 'A') array[i] = 'T';
                else if (let == 'T') array[i] = 'A';
                else if (let == 'C') array[i] = 'G';
                else if (let == 'G') array[i] = 'C';
            }

            Array.Reverse(array);
            return new string(array);
        }

        public static string StringToAminoAcid(String input)
        {
            string result = "";
            for (int i = 0; i < input.Length; i += 3)
            {
                result += codonToAminoAcid(input.Substring(i, 3));
            }
            return result;
        }

        public static string codonToAminoAcid(String codon)
        {

            for (int k = 0; k < CODONS.Length; k++)
            {
                if (CODONS[k].Equals(codon))
                {
                    return AMINOS_PER_CODON[k];
                }
            }

            // never reach here with valid codon
            return "X";
        }


        static void Main()
        {
            //then input is DNA
            string dna = "TTCGAATCCGTATTGCTTTGGTTGGTTGAGAGAGCGACCTACATTGCTAGTCAGAATAGGTGATTCACACAAAGCTTAGCACCTGGGCAGCACCCCGTGATGTAAACCTATGGGAACTAAGGGAGTCCTGCGGTTTTAGCCAGCAAGCGAGCCGGCAGGAACACTCATACCATCGGACGCGTTTGACGCCTCCCCGGAAAGGAAGTATTTGAGCCTCATTATTACGTATTGCCCGTTAGTCGACAAATCAAGCCCTCGTACGCAGCTTATTCGTACGACGTGGAGGCGTTCCCACGGGCCTAACACGATTGGAACACCACCATAGTAGTGTGGTTCAAATACCTCCTTTGGAGATCTAGAGCTTCACTCTGATTCTAGAGGCAACTTTACAATCGCTCTACGAAATTGTATGGACATCATCAACCGGATATTCTGGGGCGGTAGAATTTCTTTTGTTCGAATCGCTCTAGGCCAGGATCAAATTAATTGAATTGCGGACTCAAGGATCGCGATAGCCGACACATCGGACGCTGTAGAAAGCCAGTCTCTGGATTTAATCCACCCTCTATGTTTGACAAAGCACTAAAACGGGATAGTTTCGGGTGGTATAAGTTTCCCAAGACGATTGCATCGCAATTCATCAACAACCATGAACTTACTGTTTTAGTACTTCCACACACCTTGTTAAATTACGCCTTTACTTCATGTTGCGGTGTGTGTTAGATAGTGTGCAGCTACAAGTCTACCGCCATCGCAGCTCGGGATACCGGCAGATGAGATGGTCCTGAGCTCGTACCGGACTCAAACTTTTTCCTTTACTACCTAGGAATCGCCCATGCGAATTTGTCGGACACACACCATTACATTAACGTCACAACAGCTACTGTTAGAATTTTGCTCTTGCAAATCCTGGAAAGAGTTAAAAAAACTCTTCCGCGCGCCAATAGGGTAAATAATAGATAGCCAGACGGCTGTAAGAGGTGATGACATTTGCAACAATCATGCTGTCGCATCTTCCGCAAGTTCATGTCGCGCCTAGGCAATGGATCTGCGAATGGGGGCCACGGGGTATGAACTACGGAATTCTAAGAAAGTTGCCATCCAGAGTTAAGGGTTTGAGGCTAGTTGCATCGCTGGTAACGAACTACCTCATTACTTGGACGCGCAGTGTGACTTCACTCCTGTATAGCGATGATGCCAAGCAGGAATTAGCAAATCTGAAGAGCGTTTCCAAACTGGCCACTTGGACTGACACCTATCGCGGGGGATTTCAGCGCGTGTCGCTCTCACATGAGAGCTGCCGTCAGGAGCGGTAGAGTTTAGAGAGGAATGCGACAAACTCCCTATTCACCTCTCTGGTGATGTAAGGATATTTACGCTTAGTTCTATGCCAGGCTTAGGGCCTCTCGGAACTTTGGTGAGTCCTTATTAATTGATGCTACCTCTCCCTTACCTTCGCCCCAAGTCACGTAGAAGTACTCAATCCTGCTACATGATAATCAAATATTTCCAACGTTGGGAAATCGGTGACATCACATACTAGTTAAGAAACCACTGTCAGTGAACTTATATCCGGGGGAGAAAATCTACTAACTTACATACGCTGTGCGAGCAGTTTTCATTATAAGAAAATATACTCCCGAGGTACCGCATCAAGCACGACATTCCCGGAGAGCATAACATTTCGGTGCACCTGCTTTTGTGCGCTTGCTTGCGGTTATTTATAAACTACGCACAAGGCGCAAACCGCAGTGCGCATGTTTTCTCCGCCTGGCTAGAACTCGACATTCTCGTCAACGCCAATCTATGTGAGAGGATTTAGACCTCTGTGAAAACGAGTCCCTCTATAGAATAAATACCCAGATGCCAATGGGGGTTCTATCCGATGGCAGTGCATGGAGTGGTGGCTCCAGATTAAGGATGAGGAGAGGTAAAGATAACAGTTCGGTCGCCACGACGCGTTGCCAATCGAAATATCAGTACTAAAAGGCCCACCGCTCCGCTTTAGTCCGACTTTACATCCTGTGGAAATTGTCGAACGGAGGCTACATCGGGCTATATGAGTGTGAAAACCTATACTTCTCGCGTCGTTACTCAGTGCCGGTCTCCTGTTTCCCCCAGTCTTACGTACCCTTATTGATATTTGCTTCACGTTGAAACGTCCTAACGCAGCGTAAAGAGGTGTTTGAACCTCATTACTATAAAATCGCGATCGAAGGTAGACTACATACGCAAACGCCGAAACCCTCAGTTGGCCTTGTTGCAAGTATGGAACGTTGTAAAATTTTTCCTAGACGTTGAGCTATCGGTACAAGGTCGTTAGCGTCCTTACCCTTCACTTATATGCCCGACAAAACGCGGGTCCTAGTGCAGTGGTGGGAGCTTGGAATCCCGCAATACAAGGACAACCTGTATCTCGTTCGGCGTTCCGCGATCACTCGATCCCGAACCACTCCAAGCCTGGTTGATCAGCAAAAGCGGAAGGATGGATAAAGGGCTACTGGTTAATGGATGTAAACTTCCAATGATGAAATCCTGGAAACGAGGGATCGGGTTACGGTGGCGAACGGGGTACGGCAACGTGGCTATCTAGAGCCCGACGTTACGACTCATGTACATGCTGCTACGTGGTTGAAGCTGACGTTCAGATGAAGCAGTACTGAGTCCTAGGGCTTACTACTACTCCAATAGGTCTGGCCGGCCAGATACAAAAGTTCGTGGCGGCTCACCCCCTTTCTGGCGGGTGTAGCTTGCTGACCGGTTTGCTCGATAACACAGGCTAGCGAATAGTAATGAGGTTCGAAAACCTCTTTCCAACGACTGAAAGGGTCTACACGAACTATCTACATTTCCCCGCCCATGTCCTTCCGTCTGGTTGCTTCTGGAGATCCTTTCGCATTATACCGCAGCGTAGTGGCTCTGGCATATATGAAAAAATCCTTCTGTGGGTATTTGTGCCATCACTTATTGTTCGTACCGATATGGGATTACAAGTGCGATGTGATAATAAGCGAAGAAGCCAACATGTTACACTGTTCATGCGCTCCGGGTAATGTGCGGGCACCATGCTCAGTTCCCGCTCGCAGTTGTCACTGTCCCTGTTTCGGCACCATAATCAACATTTCCACGGCCACGCTGGTGAATAACCGAGGATACCGAAGTACAGCAAGAATGAGAGCGGGACTCCTCCATCTGCTTGTAATACGCCTTCAAGATAGTCCATAAAACGGTCGGGGTCTTGTTTCGGACTAGCCGCTTTGAAACGGTGCATAGTTGTGTCAAGTGTGGACATTGGCTTTCTATCCTCGTCAGCGATCCTCGGAAAGACTCGGGCAGTCGCCCCGAATCGTAATTAGGTAGTAGTGCGGCTCAAAAACTTCCTTCGACCTAACCGCTATAATGTTCGTAGATATAAATTTCGTTTCAGTATTAACAGGCGCACCGTATATATACGGAATGGTGTCGCCCCATTAGCTGCTCGCCAATATTTATCTAAGACCGCGCGCGTCTAGCGCCTTTAGTAGTTGCACCCGAGTATAGTAATGGGGTTCGAAGACTTCCTTCGCAAGGCTGCCATACTGTATCACAAGTACTGACGGAGCCCCGGAGGAGTGCAGGATACGGCAAAGGAGACCATTACCGGGGCATGAGTCCAAGTTAGCCCGTTAGGTGAAGGACGCTGATACAATAGTGAATCCGTTACTGAAAGGTTTAGAAGACCGGGGGGCTCGCACTAGGTCCAAATATTATGAACCCTACTCCTGCAACTGAATTGGCCGTCCAGGCGATATTTAAAAGGGGTTACTAGCAGGTTCATCGGAGCCCGTACTCCTTCCGGGCATAGTCGTTCGACGGGTAGAAATTCATCCAGTCGTGCCGGATACCCCGAGAATACCCCTATTTTTTGATCCTTCACCATCATCGTCCGCGGACTCATCTAAGTACCTCAGACCGAAACTGTTATCGTAGCGAAGAGCGAACTCGAATGACATCGCTTGTCCAACAGGGAAAATATGTAAAGTATATGCAGATTATTATAGGAAGATCACAAACTCCATCGCGCCTAGGCCAAAGACTTGCCAGAACAACATCTCTTCCAGAGCAAGGAAGTGTTTGAACCTCACTATTATCGAGAGAAGTCCCATGAATTTATAATAGTGAGGCTCAAAAACTTCCTTCATCGTCGGGCGCTGGGGCGAGCTAGGCTTCCCTAGCCGTCATTACTGTACCCACGCCAAATATTATCGAGTATGACTACGAAGCCTTCACAAGGGGCTGCAGTAACAGACTAACTCACGCACACCGCAACTACTATCCTAAATTGAGTAAGAAAACCCTCGACTATAGCCCTTGAATTAAATTCGCTATTTAAGGAAGACCGCGCTTCCGCTCGCCCGCGTATAGTTTACCAGTCCCAAGAAACATGTGTGGCCAGCCTACCTGAAGAGCTGTGTAAAGATAGATTCTGACATCCTCAAAAAGAAGTTTTCGAGCCGCACTACTACGCACGGAGCTCCGTTATTCAAGGCATGTCGAAGTACAGCGTGGTGGCCTCTCCTGTTCTCCACCCCAGCTAAACCCACCTTGTTCGAATTCGCGCAACTGTATATGACATGAACACTTACAGGGGTTAGAAGTTACTGCAACCAAGATAGAGCTCGTCGAAGTAATAGTGCGGTTCAAAAACTTCCTTCAATTGGTCTCATCACTTAAATTTAAGAGCTATTGTGAGTACAGGTACGGATGCGGCTTCAGTGGATCTTCAGCATTCATTCCTTGTAGTAATGGGGTTCGAAGACTTCCTTGCCAGGGTACCAAACAAGTCTTGCGCATCCTCCTCCCTAAGGAGGTATTTGAACCCCACTATTACCCACGATAGAACATGCAGGGTTTGATAGTGGAACACCTTTTAGAATCTGGGGATAAATTCCCAGGACTAATGTATGGCTGTAGTAATGAGGTTCAAAAACCTCCTTTTCAGGTGGATCGCAGGCCGTGCTGCCTCACAAGCTGGGACGCCGTCCACGGTATAGCCGGCGTCGGCAGTTACTGTGAAATAGCGGAAACTCGATCCCAATATATCATCTTACGTTTGGCGCCCAATAGTCGCCCAGTACCCGTTGACAGTTCTTTAACTCGGCTTAGAACTACTAGACAGGTTCAACCGAACCTTGCCCTAGTTCCCACTCCCGTAATTCATTTGGGTTTGCATCTAGAATACTGGAGGGTGCATAGACGAAACGTGTACGTCGGAGAAAACGTAAGAAAATGACCTAGACTCATAGTAGTGAGGTTCGAAGACTTCCTTTCAGTGAAATCGATCCACCACTCGCCGCGAAGAGATAATAGCATAGAGCACAAGTGCGCGAGTAGAGAAAAAGGCTATCCCAACCGGGCACGTCCTTCGTGTTTGGCGTTTACATACGGCACCCCGTTTCTGCACGTTAACCGTCTAGTATCCAACGGTGGATGGCGGACGCTAGACTATAGATATGAGATATCGAGACCTGGAGCTGGGTGTGGCTGCAGCCCGGGTCATTGCGGGCTGTGAATTCAAGGGCATGTAAACAAGCGTATATCGAACAGTGGATGGGCACCTGCAATACTCACGGTAGAGTTAGCTCACAGGATTCACGTTGAGGACTATGAGTCCCTCTTCGCTAGCAGTCTGGGGGGATATGGAGTTTAATAGCTTGACGTAGTAATGGGGCTCAAACACCTCTTTGTGTGAGCACAGCTACTTGCATTAAGAGATTCTAAACAGCGATCATCTCGGCTATTTCGGGCCAGCCTTTTCGGCAGGATGTTATGTAGCATTTCTGGAAGCTTCCCCCTCGAATCTACTAGTGGTGAGAAGATGCCCCACCGATATTACTCTTTAATCTTGAGAAACCTAAAACCGATCTGACCTCAGACGGGCGGCTCCCACCCGAGGATAAACTCGTCAATAATAATGTGGCTCGAACACTTCTTTTCTCACTAGGCTTTTACGACACGCCACATGTATTTAAGCATCTACCTAACTTGTGTCTGCTGATATACAGCGCATTCTACGCCCAACCTACCAATTACTTCAACGTAGTGCGTGGCTAAAATTCAGGGGAGCTTCATCTCTGTCTTAATTTGAAGGTTCTTCCGGGGCGTTTGGGAATCTTCGTGCCTTTTGCGAGGTTAAGGTATCAAAGAAGTTTTCGAACCACATTATTACCGCCTTAAGCACCGGCGCATCCTGCTCGTGACAACTCTACCCTGCCCTGATAAAGGCACTGAACGTTCCAGAGAGTGCATCATTGACACGCGAGCAGGCCACAGTAGCCACAAGACGTATGGGTGATTATAGAATTGGTGGAGGTGTTGTTAACGATCAGGAGGACATTAGTGGGAGTTAGGAAAGACCCTATGTTCTCTCTATCGCGGACTTGTAACTTGACAAGCAAAAGGGTAAGAGAGCTGCACACCGAAGCAGGCCCTTCCTATACCTGTTTTTCCTACGCGTAGAGAGGAATCCAGAAAGGTGATAATTGGCATTCGATGAAAAAACAGTGTGCCACTGACTTAGTTCTATATGTGAAGAGCCTGTTAGCACGTGACGGCGGCCTTGGTATAGAGCCCTTAATGGTCTCCATCGCGTAGTAATGGGGCTCGAAAACCTCCTTACTTGGGATTGCGTGGCCTCCTTGTGAGTCATACACAAGGCTTAGGGCTATGGGGCGATACACTCCTTTTCGCGGCGCATGGGGCGGTGATGCCTACATAGTAGTAGTGACTGCCTTTCTGGGGGGCTATTTGTGGATGACCAACACCTGACCAGCGATGCAATCGCTAGGGGAGGTACACCTCTCATATGTTACAACAATCACCGAATTGTGTTTCGAATTCGAATCAAGTTTGCGGTGTCGACCAGATCTGGTCTTGCTGCCATACCGGGTTCGCCGCCTCCGGTGGATAGAACTGCATCTTAAGACATCTGGACCCAGCGGTAAGTAGCGGGAAGAGTTTAGAGTCATTCGTACAACTACAGGCTAAGGGCTTACTGGGGAGTTGTTGTAGGGCATAAAGATCGCCCCATGACTTTTCGTACTTTCCCCGATAGTTCACTCGCAGCGAGCTGCGGCTGGGCTTCGCCACACGAGTACGGGCAACATTTATCTCCTCTAATCACTGGGCACCGCGCGAGGAAATAGAAAACCCTAATCAGTGCTCATGGGCGCATCTATTGGTCTCCGCATGCACGATGCCGCGGAGTGCTTAGTTGTCCCTGCATAATCTTCGTAGATGTATAAGAGATTACCTATTTATTCGGTTTCGGTTCTAGACGTACCTTGCCGCATGAGTATAGGCTAATGAACTGAGTTGGCGCCAGAGGGAAAGGCATAATAATGCGGCTCGAATACTTCCTTAAGGAAGTATTCGAACCACATTACTAT";

            //The given peptide 
            string givenPeptide = "KEVFEPHYY";
            int resultCount = 0;
            int candidateLength = givenPeptide.Length * 3;
            string forward = "";
            string backward = "";

            for (int pos = 0; pos < dna.Length - candidateLength + 1; pos++)  // Added the "+ 1"
            {
                forward = dna.Substring(pos, candidateLength);
                backward = DNAComplement(forward);

                // Unremark to get a glimpse into what is happening...
                //Console.WriteLine("pos: {0}, forward: {1}, backward: {2}, forwardTranslation: {3}, backwardTranslation: {4}",
                //    pos, forward, backward, StringToAminoAcid(forward), StringToAminoAcid(backward));

                if (
                    (StringToAminoAcid(forward) == givenPeptide)
                    ||
                    (StringToAminoAcid(backward) == givenPeptide)
                  )
                {
                    resultCount++;
                    Console.WriteLine(String.Format("Result {0,3} at position {1,6}... {2}", resultCount, pos, forward));
                }
            }

            Console.WriteLine("Done");
            Console.ReadLine();
        }//end main
    }//end class
}
+2

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