I'm doing a project, and my goal is to do alignments of a particular gene product to see if there is any conservation of secondary structures across different species.

So far, I have found a few from UniProt that are reviewed. I want to add more from different species, but the sequences were all created via AI prediction from a genome sequence.

Can I use those at all or no?

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    $\begingroup$ Welcome to Biology.SE! So, you are aligning protein sequences from some species with a known function, and you want to know if it's ok to include proteins from other species that are computationally predicted to have the same function? This is pretty standard practice, though you should expand on what you mean by "AI prediction". HMMs are common tools for searching for proteins with similar structural motifs, is that what you used? $\endgroup$
    – acvill
    Dec 3 '21 at 21:37
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    $\begingroup$ not quite, I am aligning the same gene product from different species. The gene of interest is a human gene and I am searching for homologs. I have found homolog sequences in rat and mouse, which were reviewed and backed by experimental data. If i blast this human gene against xenopus tropicalis, I get a protein sequence that is "predicated by automated computational analysis...derived from a genomic sequence...annotated using gene prediction method: Gnomon, supported by mRNA and EST evidence." I am confused by the wording here...does this protein exist or? $\endgroup$ Dec 3 '21 at 22:04
  • $\begingroup$ Thanks for the clarification. I suggest editing your question to add the information you've provided in your comment. Concerning your question -- does this protein exist -- you should read up on how Gnomon works. $\endgroup$
    – acvill
    Dec 3 '21 at 22:08
  • $\begingroup$ I did read that link before posting here...and I got the idea that the the answer is highly likely...I also have read the Refseq FAQ regarding the xp prefix (most of my sequences' accession number starts with that since they were all predications)...but I am still unsure... $\endgroup$ Dec 3 '21 at 22:23

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