c# - 如何完成获取编码给定氨基酸序列的基因组的子字符串-6ren

c# - 如何完成获取编码给定氨基酸序列的基因组的子字符串

转载作者：行者123 更新时间：2023-11-30 12:28:55

肽编码问题在于寻找编码给定氨基酸序列的基因组子串。

遗传密码描述了将 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、第 2 和第 3 个核苷酸。第 4、5 和 6 圈以三种方式定义翻译的氨基酸:氨基酸的全名、它的 3 个字母缩写和它的单字母缩写。总共 64 个 RNA 密码子中的三个是终止密码子，它们会停止翻译并隐式地在氨基酸字母表中添加第 21 个终止符号。

enter image description here

问题在于有

输入:一个 DNA 字符串 Text 和一个氨基酸字符串 Peptide。

和

输出:Text encoding Peptide 的所有子串(如果存在这样的子串)。

Sample Input:
     ATGGCCATGGCCCCCAGAACTGAGATCAATAGTACCCGTATTAACGGGTGA
     MA

Sample Output:
     ATGGCC
     GGCCAT
     ATGGCC

结果是读取三元组得到的，所以，ATGGCC encodes MA，GGCCAT inverse 就是 CCGGTA 反写，所以实际上是 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好的数组

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

但是我只得到:

AAGGAAGTATTTGAGCCTCATTATTAC
AAAGAGGTGTTTGAACCTCATTACTAT
AAGGAAGTGTTTGAACCTCACTATTAT
AAAGAAGTTTTCGAGCCGCACTACTAC
AAGGAGGTATTTGAACCCCACTATTAC
AAAGAAGTTTTCGAACCACATTATTAC

我在想问题，看来问题是我不是每次都循环所有字符串...

最佳答案

看起来问题有两个方面。您的外部 for 循环还不够远，无法捕捉到 dna 字符串的末尾。其次，反转单个密码子似乎不起作用，您必须在获得补码之前获取整个 (givenPeptideLength * 3) 字符串。以下更改输出您在示例中输入的字符串，因此我希望它能满足您的要求。它还具有更加简洁的好处。

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
}

关于c# - 如何完成获取编码给定氨基酸序列的基因组的子字符串，我们在Stack Overflow上找到一个类似的问题： https://stackoverflow.com/questions/20209067/

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c# - 如何完成获取编码给定氨基酸序列的基因组的子字符串