How to create alignment of UTR's for use in TargetScan?

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5.1 years ago

jon.brate ▴ 310

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 • 1.5k views

ADD COMMENT • link 5.1 years ago by jon.brate ▴ 310

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Hey Jon,

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

ADD REPLY • link 4.9 years ago by mollitz ▴ 90

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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 REPLY • link 4.9 years ago by jon.brate ▴ 310

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