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Question for Geneticists & Biologists about DNA sequence nomenclature?
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<blockquote data-quote="LazarusLong42" data-source="post: 1400978" data-attributes="member: 9620"><p>Shemeska: I totally agree with you... with my BS in chemistry but working as a molecular biologist, it gets to be a pain. Now, there are IUPAC names for proteins, of course. But do you <em>really</em> want to deal with a name like:</p><p></p><p>methionylprolylglycylglycylarginylarginylarginylglycylleucylvalylalanylprolylglutaminyl etc etc... ?</p><p></p><p>(The first few AA of the 1174-aa protein we work with. I'd rather just call it EAG.) And hell... even that uses trivial names, rather than calling glutamine 2-amino-4-carbamoylbutanoic acid.</p><p></p><p>The major problem is that the further you shorten the name, the less information you are indicating about the molecule in question.</p><p></p><p>Now, for genes:</p><p></p><p>(1) Probably the only genes we can construct systematic names for would be in those where there's already a full or nearly-complete genome sequence for the organism in question.</p><p></p><p>(2) We could probably pinpoint a gene by summing up as: Species-Chromosome-P/Q-distance from centromere. But even this is quite imprecise... where do we define the centromere as ending? How do you determine which strand is the sense strand? How do you label the exons... and so forth.</p><p></p><p>The only way to do it, it seems, is to keep a database of the information in question (GenBank/Entrez) and make that database as easily searchable as possible. The former works pretty well; the latter is less than finished. <img src="https://cdn.jsdelivr.net/joypixels/assets/8.0/png/unicode/64/1f642.png" class="smilie smilie--emoji" loading="lazy" width="64" height="64" alt=":)" title="Smile :)" data-smilie="1"data-shortname=":)" /></p></blockquote><p></p>
[QUOTE="LazarusLong42, post: 1400978, member: 9620"] Shemeska: I totally agree with you... with my BS in chemistry but working as a molecular biologist, it gets to be a pain. Now, there are IUPAC names for proteins, of course. But do you [i]really[/i] want to deal with a name like: methionylprolylglycylglycylarginylarginylarginylglycylleucylvalylalanylprolylglutaminyl etc etc... ? (The first few AA of the 1174-aa protein we work with. I'd rather just call it EAG.) And hell... even that uses trivial names, rather than calling glutamine 2-amino-4-carbamoylbutanoic acid. The major problem is that the further you shorten the name, the less information you are indicating about the molecule in question. Now, for genes: (1) Probably the only genes we can construct systematic names for would be in those where there's already a full or nearly-complete genome sequence for the organism in question. (2) We could probably pinpoint a gene by summing up as: Species-Chromosome-P/Q-distance from centromere. But even this is quite imprecise... where do we define the centromere as ending? How do you determine which strand is the sense strand? How do you label the exons... and so forth. The only way to do it, it seems, is to keep a database of the information in question (GenBank/Entrez) and make that database as easily searchable as possible. The former works pretty well; the latter is less than finished. :) [/QUOTE]
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