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How to identify transposons in a non-model organism transcriptome

I have several assembled, annotated transcriptomes of non-model organisms (fish). I would like to identify what transposons are present in these transcriptomes (LTR, SINEs, LINEs etc) and compare them. I am currently trying to use RepeatMasker to identify them using a clade specific library from RepBase but I was thinking of trying to look for them de novo with REPET. Just looking for suggestions and ideas really. Thank you.

rna-seq next-gen blast
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updated by Biostar Biostar • written by pdm37 • pdm37

1 answer

Tandem Repeat Finder is also a good option for finding denovo repeats.

You can also try, Censor for finding different kinds of repeats from your sequences. Check this paper analysing transposons using censor and repeatmasker.

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updated by Ram Ram • written by Prakki Rama Prakki Rama

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