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Detection Transposable Elements in eukaryote

is any one here can recommend me a tool or pipline that can help to identify and characterize the transposable element in a mammal genome "Scaffold" level without a reference ?

transposable element
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updated by corend corend • written by bioinfo • bioinfo

OmicsTools have listed 100+ tools for the same. You can choose one of them appropriate to your work.

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written by Nitin Narwade Nitin Narwade

must of these tools outdated and require a reference to as an input

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written by bioinfo • bioinfo

2 answers

as far as i been trying the suitable tool for the job is LTRharvest, Transposable has been detected now how to classify them and annotatie them in fact they are from non reference genome and for this job Ltrdigest is recommended

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written by bioinfo • bioinfo

You should give a look at this paper.

My personal advise would be to use repeat modeler.

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written by corend corend

highly appreciate your comments

but I have tried repeat modeler and I have created my own library, then I run the library against my genome with repeat masker, but output only simple repeats and low complexity, none of the LTR has been detected

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written by bioinfo • bioinfo

Is it repeat modeler or repeat masker that do not find them? Repeat modeler only finds what is repeated. If a LTR is old and present in only one copy, it might remain undetected by repeat modeler. Then you should use LTRharvest that uses the structure of the LTR to detect it and not it's repeated nature, and add it to the TE library.

If it's present in the library but that repeat masker does not find it, it sounds very strange, I never had this kind of issue. Have you tried to blast the LTR that is not found directly on the genome?

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written by corend corend

the detection has done by using ltrharvest then annotate the LTR candidates with protein domain search "Hmm" then filter the candidates, remain only those with protein hits, around 179, I extract the fasta sequences from all the filtered LTR, then I cluster them using vmatch but the clustering percentage only 27 %.

I wanna Run Blastn to confirm the candidates? is this step correct and does blastn can run against TE databases? how can I classify them into families and conclude my Results

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written by bioinfo • bioinfo

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