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The reason I am asking this is the following. Some time ago I performed proofreading of a book, and there was a phrase containing "Protein-encoding genes". I wrote a post on my blog, detailing why this is wrong, according to the assumption that "to code" means to write something in a given standard representation (like "I code a program" in the sense that I write a program in a standard representation of a programming language). Another example is Huffman coding, which is an algorithm for compression. To encode, on the other hand, means to transform something into something else, for example, base32 encoding transforms binary data into text, so it is possible to send it via email.

Now I am not really sure about it anymore. What I can say for sure, is that genes do not perform any operation, they just store information, so to me "Protein-coding genes" makes a lot more sense than "Protein-encoding genes". I don't understand, in particular, the exact grammar of suffixes like "-coding". Is it a verb, an adjective, or something I'm not aware of ?

  • I am not quite sure about protein-coding vs. protein-encoding, the more so that I am not a native English speaker. I would like just to mention that genes either encode proteins or code for them. – user113209 Mar 10 '15 at 14:35
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Regarding usage, two metrics point towards “protein-coding gene” being used more than “protein-encoding gene” by a factor of 2 or 3. The two searches I did where a competitive Google Scholar search, and a standard Google search restricted to the .edu top-level domain (which should restrict to academic sources of information).

Next, regarding grammar, -coding is not a suffix. It is a noun + gerund compound, used adjectivally. You are talking about a gene that codes a protein, your verb is code, your noun is protein, so the compound is “protein coding”. You would say, for example, that protein coding is one of the functions of the gene. When used adjectivally, you add a hyphen, and say: this is a protein-coding gene.

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The NOAD reports the meaning that encoding and coding have in biochemistry.

  • encode (verb): be responsible for producing a substance or behavior;
  • coding (noun): the process of coding genetically for an amino acid, protein, or characteristic.

Coding is generally defined as the process of assigning a code to something for the purposes of classification or identification.

Looking for sentences that contains coding in the Corpus of Contemporary American, I find the following sentences:

A gene is the hereditary unit such as a segment of DNA coding for a specific protein. Human beings have about 80,000 genes, and we are more than ninety-nine percent identical in our genetic makeup.

Moreover, there are large segments of nonfunctional DNA between genes (i.e., between segments with known coding or regulatory roles). The existence of introns and other nonfunctional DNA segments makes it impossible to simply read off a DNA sequence and predict an amino acid sequence (even when all regulatory regions are known).

Looking for encode, I obtain the following sentences:

The gene encodes a cell-surface protein dubbed CED-1, which resembles the scavenger receptors in people. Whether the protein recognizes phosphatidylserine or another eat-me sign on a worm's apoptotic cells remains a mystery.

The mammalian proglucagon gene encodes three related sequences, glucagon and the glucagon-like peptides 1 and 2 (GLP-1 and GLP-2), of which has an essential role in metabolism. A family of closely related receptors mediates the physiological actions of these hormones.

Thanks to the efforts of Paul Hebert at the University of Guelph in Canada, a broad consensus has been reached regarding the gene that is the primary focus of this effort: the cytochrome c oxidase subunit1 (CO1) gene encoded in the mitochondrial DNA.

Saying it with simple words, coding refers to the process, while encode refers to the action of doing that process.

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