Question: Suggestions for LTR family level classification
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4.7 years ago by
European Union
rimjhim.roy.ch70 wrote:

I have a list of 7000 LTRs predicted using LTR harvest and LTR digest run on a plant genome. I want to do LTR dynamics analysis, therefore I need the elements having two intact LTR to be grouped into families.

Is there a better way to group them into families other than homology based BLAST approach? The sequences are too different from it's nearest relatives in Repbase.

Is it advisable to cluster them before and then work on the protein domains to group them? I am just looking for suggestions.

Thanks a lot

ADD COMMENTlink modified 4.1 years ago by rakeshmbb0 • written 4.7 years ago by rimjhim.roy.ch70

Can you please guide me how can I install and use LTR harvest. Looking forward for your respnse

ADD REPLYlink written 4.1 years ago by rakeshmbb0
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