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I have gene sequence of a ton of individuals within a subspecies from cdna and the ncbi IDed sequence as well. Is there any way to tell using just the sequence that the gene for an individual is non-function or only partially functional?

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In general, no. There might be specific cases where you can, like if there is a stop codon, or a frameshift mutation early on, or someone else has seen your exact variant and experimentally proved that it has no function.

But in general, you cannot predict function from in silico data alone.

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It is possible to get a prediction of the change caused by a mutation using programs like Sift or polyphen(only for human proteins), but these are only rough estimates

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I don't know your level of knowledge, so this may seem very obvious to you, but...

  • Translating it into the six frames gives you some hints. If the sequence has degenerated and is full of stop codon, then it's nonfunctional.

  • Align the sequences with Mega or AliView or whatever, then translate them. If there is a frameshift mutation in your sequence, it becomes very visible within the alignment and chances are that the sequence isn't functional anymore.

  • Find information about the protein's domain in Pfam and look closely to the alignments in the functional domain. If otherwise conserved residues are mutated, this should ring a bell. (Since all your sequences will be very similar to each other, you may want to add some sequences of the protein of other species, so that you can find more easily the active residues within a domain)

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