Question: How to identify transposons in a non-model organism transcriptome
1
gravatar for pdm37
5.0 years ago by
pdm3710
United States
pdm3710 wrote:

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.

blast rna-seq next-gen • 1.7k views
ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 5.0 years ago by pdm3710
1
gravatar for Prakki Rama
5.0 years ago by
Prakki Rama2.2k
Singapore
Prakki Rama2.2k wrote:

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.

 

ADD COMMENTlink written 5.0 years ago by Prakki Rama2.2k
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