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/

文章推荐： c# - bin中的dll与vs2012中发布的dll有区别吗

文章推荐： ios - Realm 缓慢插入数据(主键 UUID().uuidString)

文章推荐： javascript - 如何使用 Xpages onchange 事件激活按钮

Python:过滤器(函数，序列)和映射(函数，序列)之间的区别
我正在阅读 Python 文档以真正深入了解 Python 语言，并遇到了 filter 和 map 函数。我以前使用过过滤器，但从未使用过映射，尽管我在 SO 上的各种 Python 问题中都见过这
algorithm - 给定一个 preOrder 和 inOrder 序列，可能有多少级阶 BST 序列？
当我尝试打印 BST 的级别顺序时，这个问题提示了我。这是一个 Pre-Order Sequence: 4, 1, 2, 3, 5, 6, 7, 8 In_order Sequence : 1, 2
c++ - 定义函数后 main 出错？ "undefined reference to ' 序列::序列()'"
我的代码在 main(序列测试；)的第一行出现错误，指出它是对 sequence::sequence() 的 undefined reference 。我无法更改 main 中的代码。有谁知道我该如何
latex 序列\/?
这可能很简单，但我在通常的 latex 指南中找不到任何相关内容。在这句话中: {\em hello\/} “\/”的目的是什么？最佳答案这就是所谓的斜体校正。其目的是确保斜体文本后有适当的间距。
Postgresql 序列
当我从 Postgresql 表中删除所有记录，然后尝试重置序列以在插入时开始一个编号为 1 的新记录时，我得到不同的结果: SELECT setval('tblname_id_seq', (SELE
30、MariaDB 序列
在版本10.0.3中，MariaDB引入了一种称为序列的存储引擎。其ad hoc为操作生成整数序列，然后终止。该序列包含正整数，以降序或升序排列，并使用起始，结束和递增值。它不允许在多个查询中
数字的 Groovy 序列
如何在 Groovy 中获取给定数字的序列，例如: def number = 169 // need a method in groovy to find the consecutive number
作为特定复杂类型的扩展的任何类型元素的 xsd 序列
基本上，如果这是 .NET，它看起来像这样: ISomething { string A { get; } int B { get; } } var somethings = new List
非阻塞赋值的 Verilog 序列
说以下代码部分(同一块): A <= 1 A <= 2 变量 A 总是被赋值为 2 吗？还是会出现竞争条件并分配 1 或 2？我对非阻塞赋值的理解是，由硬件在 future 分配变量 A，因此它可能
WiX Action 序列
在运行 WiX 设置时，我正在寻找操作列表及其顺序。不知何故，官方网站似乎没有提供任何信息。基本问题是我想正确安排我的自定义操作。通常我需要使用 regsvr32.exe 注册一个 DLL，而这只能
具有至少一个元素的 F# 序列
F#初学者在这里我想创建一个类型，它是具有至少一个元素的另一种具体类型(事件)的序列。任何其他元素都可以在以后随时添加。通常在 C# 中，我会创建一个具有私有(private) List 和公共(p
sql - 在Oracle中删除所有用户表/序列
作为构建过程和不断发展的数据库的一部分，我试图创建一个脚本，该脚本将删除用户的所有表和序列。我不想重新创建用户，因为这将需要比所允许的更多的权限。我的脚本创建了一个过程来删除表/序列，执行该过程，然
日期和向量的 R 序列
我想恢复两个向量的第一个日期和相同向量的第二个日期之间的日期序列，.... 这是一个例子: dates1 = as.Date(c('2015-10-01', '2015-03-27', '2015-0
SQL ORDER BY(序列)
这个问题已经有答案了: sql ORDER BY multiple values in specific order? (12 个回答) 已关闭 9 年前。我有一个 sql 语句，我想要ORDER
日期和向量的 R 序列
我想恢复两个向量的第一个日期和相同向量的第二个日期之间的日期序列，.... 这是一个例子: dates1 = as.Date(c('2015-10-01', '2015-03-27', '2015-0
java - 如何在java中转义],[序列？
在用java编写代码时，我需要用“],[”分割字符串。下面是我的代码。 try (BufferedReader reader = new BufferedReader(new InputStreamR
数字的 Collatz 序列
这个问题已经有答案了: Project Euler Question 14 (Collatz Problem) (8 个回答) 已关闭 9 年前。我正在尝试查找数字的 Collatz 序列。以下
C++:使用循环和变量模式(序列)
我有一个例程函数process_letter_location(const char& c, string &word)。在我的 main 中，我声明了一系列字符串变量，如下所示: string s
c++ - 最长的多米诺骨牌链/序列
我需要找到最长的多米诺骨牌链，给定一组 12 个随机挑选的多米诺骨牌。我已经递归地生成了多米诺骨牌的所有可能性(使用 0 到 12 的面值有 91 种可能性)。多米诺骨牌由一 block “砖 blo
c++ - 序列 vector
我有这个数据结构 Seq，它继承了类 vector 但有一些额外的功能。使用这个数据结构 Seq 我有这个预定义的数据结构: typedef Seq > MxInt2d; 我现在想要一个包含多个 Mx

行者123

个人简介

我是一名优秀的程序员,十分优秀！

作者热门文章

滴滴打车优惠券免费领取

全站热门文章

首页

博学

6Ren·AI

商城

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