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Repeats/Transposons finding

Hey, I am actually very new to this and I have few genomes to analyse. I am looking through many methods, could anyone please suggest me any good method (reliable but relatively easy to use) for identifying repetitive DNA/ transposons?

repeats genome transposons genomics
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written by Jaykumar • Jaykumar

1 answer

If you have large sequences to analyse, you can download the RepeatMasker app and it will be able to identify the different classes of transposons and repeat elements. RepeatMasker requires a proprietary sequence database called repbase, which can be restrictive. If you want to avoid repbase/repeatmasker there are now some alternatives like DFAM. Links below.

https://www.repeatmasker.org/RepeatMasker/

https://github.com/HullUni-bioinformatics/TE-search-tools

https://dfam.org/home

https://bioinformatics.stackexchange.com/questions/343/are-there-any-repbase-alternatives-for-genome-wide-repeat-element-annotations

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written by mark.ziemann mark.ziemann

Thank you very much, Mark. I will try them. :)

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written by Jaykumar • Jaykumar

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