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PORepresenting the DNA alphabet in C with typedef and enum
 

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  1. PORepresenting the DNA alphabet in C with typedef and enum
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    <p>I'm writing a program that processes genetic sequence and I want to store each nucleotide in a byte where each bit represents one of the letters of the genetic alphabet <code>A,C,G,T</code> (only half of the bits will be used evidently).</p> <p>My encoding is the following:</p> <pre><code>A = 0b1000 C = 0b0100 G = 0b0010 T = 0b0001 R = 0b1010 Y = 0b0101 N = 0b0000 </code></pre> <p>Here, <code>R</code> are purines, which can stand for <code>A</code> or <code>G</code>, <code>Y</code> are pyrimidines (<code>C</code> or <code>T</code>), and <code>N</code> could stand for either letter.</p> <p>What is the best way to define this format in C using <code>typedef</code> and <code>enum</code>? I would like to define a type that allows me to assign a letter to a variable by name such as</p> <pre><code>typedef ... nucleotide_t; nucleotide_t x[] = {G, A, T, T, A, C, A}; </code></pre> <p>Edit: Thanks for the input. I definitely have my reason for not wanting strings, but thanks for the suggestion. It's true that logically, <code>N</code> should be <code>0b1111</code> but for my application it does make more sense to represent it as <em>none of the above</em>.</p> <p>Please note that I <em>do</em> have an idea how to make this work, but I don't break out the ol' C too often and I'm rather looking for what the most elegant solution is. I guess if I want to reserve the <code>NUL</code> byte, then I could just add <code>0b10000</code> to my code everywhere.</p> <p>I think the two possible ways to go are either an <code>enum</code> or some <code>#define</code> macros. Yet, enums are <code>int</code> and I need a <code>char</code>, so are macros the better solution?</p>
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    1. COPerhaps you could use something like `#define A (0b1000)` or `#define A (0x8)`. Share and enjoy.
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      1. USBob Jarvis
    2. CO+1 for the title - reminds me of old 19th century British travelogue's such as "Across Africa With Cannon And Butterfly Net".
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      1. PORepresenting the DNA alphabet in C with typedef and enum
      1. USBob Jarvis
    3. COUnless this kind of encoding greatly improves performance, I would just use ASCII characters. That way you can use `strstr` and similar functions that work on null-terminated strings. If you do need the bit patterns to have special meaning, you might at least avoid using the value 0 so that you can still use string functions on your sequences.
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