Repeats/Transposons finding

Question

[Jaykumar]

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?

Answer 1

[mark.ziemann]

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

[Jaykumar]

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