Translation for genes with introns
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3.5 years ago
DNAlias ▴ 40

I used tBLASTn to find a homolog for a human RefSeq gene in an unannotated genome. I want to find the corresponding protein sequence, but I'm not sure what is the best way to do this for Eukaryotic genes because they can have introns. Is there a particular program or method that I can use without annotating the whole genome?

Thank you

translation eukaryote • 593 views
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My instinct is to back translate and then to align the two nucleotide sequences, with manual adjustments if there are any small indels, cut out large gaps representing potential introns, translate the resulting sequence, and align the new protein sequence to the original protein sequence for the query to verify. Please let me know if there is a better or more streamlined way to do this.

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