Repeats/Transposons finding
1
3
Entering edit mode
2.4 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 • 947 views
ADD COMMENT
4
Entering edit mode
2.4 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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2742 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6