二进制编码的DNA [英] Binary to DNA encoding

问题描述

我有一个8位二进制序列。我需要带code这8位二进制序列到DNA序列。

如，我有 10011100 ，我在下面的编码规则，

  A = 00，T = 11; G = 10; C = 01，
 

所以，我希望它是这样的 GCTA 。因此，我需要4位的DNA序列作为结果。

我需要为256 * 256的矩阵，其中每个元素是一个8位二进制序列做到这一点。

我用下面的code产生的矩阵

  A = imread（'C：\\用户\\桌面\\ lena.png'）;
DISP（一）;
imshow（一）;
对于i = 1：1：256
    对于j = 1：1：256
        B {I，J，1} = DEC2BIN（一（I，J），8）;
    结束
结束
DISP（二）
 

解决方案

下面是给你一个没有为循环的方法。我们可以真正做到这三行。

您有第一步骤，其是采取映像中的每个8位数字，并把它转换成其二进制重新presentation。注意到，这是一个二维单元阵列，其大小如你用来做这种转换的图象相同。每个单元阵列将是数字的重新presentation的作为字符串

现在，你现在真正需要做的就是创建一个查询，然后使用该查询生成一个新的2D单元阵列每个位置四个大字。因此，我会使用 容器。地图（） 类来创建每对位被映射到一个字符一个键 - 值查找。一旦我们做到这一点，我们就可以使用 cellfun 并遍历您的单元阵列中的每个8字符串，比特分解成2元字符串，并使用这些作为键进入我们的查找。我们难免会4个独立的细胞的输出，所以我们需要使用 cell2mat 把它全部重新走到一起。因此，尝试做这样的：

  codebook = containers.Map（{'00'，'11'，'10'，'01'}，{'A'，'T'，'G '，'C'}）; ％// 抬头
outputCell = cellfun（@（x）的值（codebook，{×（1：2）中，x（3：4），X（5：6）中，x（7：8）}），...
             B，'单向'，0）;
finalOutput = cellfun（@ cell2mat，outputCell，'单向'，0）;
 

作为一个例子，假设我们有这个2×2的细胞元素矩阵：

  B = {'11111111'，'10101010'; '11001100'，'00001101'}b =1111111110101010
1100110000001101
 

通过上面的code运行，这就是我们得到：

  finalOutput =TTTT'GGGG
TATA'AATC
 

I have an 8 bit binary sequence. I need to encode this 8 bit binary sequence into DNA sequence.

E.g., I have 10011100, the encoding rule I'm following is,

A=00;T=11;G=10;C=01,

So I want it to be something like GCTA. Therefore I need 4 bit DNA sequence as result.

I need to do this for a 256 * 256 matrix where each element is an 8 bit binary sequence.

I've created the matrix using the following code

a=imread('C:\Users\Desktop\lena.png');
disp(a);
imshow(a);
for i=1:1:256
    for j=1:1:256
        b{i,j,1} = dec2bin(a(i,j),8);
    end
end 
disp(b)

解决方案

Here's a no for loop approach for you. We can actually do this in three lines.

You have the first step which is to take each 8-bit number in your image and convert it into its binary representation. Take note that this is a 2D cell array that is the same size as the image you used for doing this conversion. Each cell array would be the representation of the number as a string.

Now, all you really need to do now is create a lookup, then use this lookup to generate four characters per location in a new 2D cell array. As such, I would use the containers.Map() class to create a key-value lookup where each pair of bits gets mapped to a single character. Once we do this, we can then use cellfun and iterate over each 8 character string in your cell array, break up the bits into 2 element strings, and use these as keys into our lookup. We will inevitably get 4 separate cells for the output, so we'll need to use cell2mat to bring it all back together. As such, try doing this:

codebook = containers.Map({'00','11','10','01'},{'A','T','G','C'}); %// Lookup
outputCell = cellfun(@(x) values(codebook, {x(1:2),x(3:4),x(5:6),x(7:8)}), ...
             b, 'uni', 0);
finalOutput = cellfun(@cell2mat, outputCell, 'uni', 0);

As an example, let's say we had this 2 x 2 matrix of cell elements:

b = {'11111111', '10101010'; '11001100', '00001101'}

b = 

'11111111'    '10101010'
'11001100'    '00001101'

Running through the above code, this is what we get:

finalOutput = 

'TTTT'    'GGGG'
'TATA'    'AATC'

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