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Biologists use the sequence of letters A, C, T and G to model genomes. A gene is a substring of a genome that begins after the three-character ATG and ends before the three-character TAG, TAA, and TGA. Therefore, the length of the genome string is a multiple of 3, and the gene does not include three characters such as ATG, TAG, TAA and TGA.

I'm a little confused by the last sentence. Take a genome as an example, ATGTTGATATATTAG. Is TTGATATAT a gene? When the definition says the gene doesn't include ATG, TAG, TAA or TGA, does this requirement apply for every three characters TTG ATA TAT or for any character TTGATATAT?

ps: I don't have too much biology background. I'm currently doing a programming assignment on gene. The definition is all that is given to me. So excuse me if my question sounds really dumb...

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    $\begingroup$ Welcome to Stack Exchange Biology. Please finish reading the Tour to find out how this site works. It is primarily for "biology researchers, academics, and students", so if you "don't have too much biology background" you should play by the rules to justify posting here. This involves reading the Help on asking questions where you will see that posters are required to research their topic. The quotation you present (citation?) is unadulterated nonsense, as reading the Wikipedia entry for "Gene" would inform you. Please do so. (PS the answer is NO.) $\endgroup$
    – David
    Oct 5, 2022 at 16:07
  • $\begingroup$ I'd suggest reading more about genome annotation and gene finding for perspectives about these as computational problems. For your specific question, Bryan's answer should sort you out with regard to how codons can translate into protein outputs. This seems like a weird definition of either gene or genome, possibly there is more context in your instructor's questions that is missing. $\endgroup$
    – Maximilian Press
    Oct 5, 2022 at 16:47
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    $\begingroup$ The premise of the question should be accepted or the question closed. The existing answers don't even attempt to answer the question (the answer is "every three characters"). $\endgroup$
    – Peter Mortensen
    Oct 6, 2022 at 0:30
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    $\begingroup$ As a programmer, I'm irked by the fact that ATGATGA follows the "definition" of gene as indicated, yet its length is not a multiple of three. $\endgroup$
    – Vorbis
    Oct 6, 2022 at 7:22

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This is a very lazy (biologically) "programmer's definition" of a gene. It would be like if you found a biology textbook that said "a program in C is everything between main( and )" - maybe for some purpose this definition is useful, but it would be clear to a programmer that it is incomplete and misses too much.

You can read about "start codon", "stop codon" and "genetic code" to understand the concepts they are using for your programming assignment. Using these concepts, there is a specific 3-letter code that says start and codes one amino acid, and every 3 letters after that codes another amino acid, until you reach a 3-letter code that indicates "stop". So, if you want to simply write a program to get an amino acid sequence from DNA/RNA this is sufficient.

For your assignment, you probably want to find what your instructor wants you to define as a gene, not what a biologist would.

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This isn't the definition of a gene. In many organisms, genes include introns, and the regions upstream and downstream of the starts and stops (untranslated regions, usually called 5' and 3' UTRs), as well as promoters upstream of the 5' UTR, are counted as part of the "gene". And of course, not all organisms always use ATG as the start codon, I'm pretty sure that some organisms have different stop codons.

But most importantly, if you looked up just the coding region of a gene, you'd definitely include the starting codon, because that's usually included in the final protein, and you'd want to include the final stop so you know you aren't looking at a truncated sequence.

That paragraph has nothing to do with how any real computational biologist would work with gene sequences. It's just pretend.

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According to the cringe-worthy biology from your assignment, yes the example that you gave - i.e. TTGATATAT - is a gene. The TGA that's out of phase (TTGATATAT) isn't relevant.

As for what makes the text that you quoted text so painful? I think it boils down to the line:

Therefore, the length of the genome string is a multiple of 3

If you're interested, a small amount of reading about the genomes of humans (or any other organism) should quickly reveal why it's nonsense.

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    $\begingroup$ note that a) that conclusion (in the given question) doesn't even follow from the rest of it, and b) i'm pretty sure they mean the gene string, not the genome string $\endgroup$
    – somebody
    Oct 8, 2022 at 6:15
  • $\begingroup$ true, my intent was to try to answer the question as posed (while also lending some color to the tone of the answers so far - mine included) $\endgroup$
    – Ben
    Oct 12, 2022 at 23:04

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