How to create alignment of UTR's for use in TargetScan?
Hi,
I want to run TargetScan on a non-model species. I have transcriptomes of several closely related species and can extract the UTRs. But I am not sure what's the best way to create the necessary alignment? I guess I have to first identify the correct homologous UTRs and give them the same name across species? And also retain the aligned sequences.
Anyone have attempted this before?
Thanks,
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Hey Jon,
did you achieve your goal and want to share your experience with us?
Hey, No, haven't done any more on this yet. But I guess what I will do is to run OrthoFinder or some other tool to identify orthologues. And then simply align the UTR's of each ortholog using MAFFT or something. But the exact procedure I haven't figured out yet. Let me know if you will do something similar.
Jon