Repeats/Transposons finding
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2.3 years ago
Jaykumar ▴ 50

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 • 926 views
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2.3 years ago
mark.ziemann ★ 1.9k

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

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