Question: How to create alignment of UTR's for use in TargetScan?
2
gravatar for jon.brate
19 months ago by
jon.brate250
Norway
jon.brate250 wrote:

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,

mirna targetscan • 534 views
ADD COMMENTlink written 19 months ago by jon.brate250

Hey Jon,

did you achieve your goal and want to share your experience with us?

ADD REPLYlink written 17 months ago by mollitz70

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

ADD REPLYlink written 16 months ago by jon.brate250
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