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REPETDB

REPETDB is a database of transposable elements. Reference sequences for various species are stored with the Intermine data warehouse framework.


Reference transposable elements are presented with their evidences allowing to determine their classification according to PASTEC , the classifier of the REPET package. Transposable elements can be queried and visualized using the powerful capabilities of Intermine

Most of the REPETDB datasets also provide the consensus copy annotation on genome via a Track Hub referenced on Track Hub Registry .

 

Refer to the   documentation for more information about the REPETDB data submission.

How to use REPETDB

Refer to use cases for using RepetDB

 

Blast sequence against RepetDB consensus database  

  • Select the "Repeats" group
  • All the results have 2 links
    • download the matching consensus sequence
    • Link to the matching consensus card in RepetDB

RepetDB citation

Amselem et al, RepetDB: a unified resource for transposable element references. Mobile DNA. 2019;10:6.

Update: 28 Feb 2022
Creation date: 02 Jun 2017