如何完成获取编码给定氨基酸序列的基因组子串

肽编码问题在于寻找编码给定氨基酸序列的基因组子串。

遗传密码描述了 RNA 3 聚体（密码子）翻译成 20 种不同氨基酸之一的过程。前三个圆圈从内向外移动，代表给定密码子的第 1 个、第 2 个和第 3 个核苷酸。第 4、5 和 6 圈以三种方式定义翻译后的氨基酸：氨基酸的全名、三字母缩写和单字母缩写。 64 个总 RNA 密码子中的 3 个是终止密码子，它们会停止翻译并隐式在氨基酸字母表中添加第 21 个终止符号。

问题在于有

输入：DNA 字符串文本和氨基酸字符串肽。

and

输出：文本编码肽的所有子串（如果存在任何此类子串）。

Sample Input:
     ATGGCCATGGCCCCCAGAACTGAGATCAATAGTACCCGTATTAACGGGTGA
     MA

Sample Output:
     ATGGCC
     GGCCAT
     ATGGCC

结果是通过读取三元组得到的，ATGGCC 编码 MA, GGCCAT逆将是 CCGGTA 向后写，所以它实际上是ATGGCC（CCGGTA.反向）

遗传密码的补码是C-G、G-C、T-A和A-T

所以为了解决这个问题我首先使用已经定义的数组

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

我应该得到

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

然而我只得到：

AAGGAAGTATTTGAGCCTCATTATTAC
AAAGAGGTGTTTGAACCTCATTACTAT
AAGGAAGTGTTTGAACCTCACTATTAT
AAAGAAGTTTTCGAGCCGCACTACTAC
AAGGAGGTATTTGAACCCCACTATTAC
AAAGAAGTTTTCGAACCACATTATTAC

我正在思考问题，问题似乎是我没有每次都循环所有字符串......

看起来问题有两个方面。你的外部 for 循环不够远，无法捕获 DNA 字符串的末端。其次，似乎反转单个密码子不起作用，并且您必须在获得补码之前获取整个 (givenPeptideLength * 3) 字符串。以下更改会输出您在示例中放入的字符串，因此我希望它能达到您想要的效果。它的优点是更加简洁。

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
}