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RepetDB: a unified resource for transposable element references.

Joëlle Amselem1, Guillaume Cornut1, Nathalie Choisne1

  • 1URGI, INRA, Université Paris-Saclay, 78026 Versailles, France.

Mobile DNA
|February 6, 2019
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Summary

RepetDB is a new database for storing and retrieving transposable elements (TEs) with classification evidence. This tool aids in analyzing genome plasticity and evolution by providing standardized TE annotations across species.

Keywords:
DatabaseRepetDBTransposable element

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Evolution

Background:

  • Transposable elements (TEs) are key drivers of genome plasticity and evolution.
  • Automated de novo annotation of TEs is crucial due to increasing genome sequencing data.
  • Existing TE databases lack classification evidence and comprehensive biological information.

Purpose of the Study:

  • To develop a standardized database for storing, retrieving, and analyzing transposable elements (TEs).
  • To provide evidence-based classification for TEs identified through de novo annotation.
  • To facilitate cross-species comparisons of TE content.

Main Methods:

  • Developed RepetDB using the InterMine data warehouse framework.
  • Integrated GnpIS genetic and genomic information system.
  • Implemented a worldwide data discovery portal for TE data access.

Main Results:

  • RepetDB stores and retrieves detected, classified, and annotated TEs in a standardized format.
  • The database provides evidence to justify TE classification.
  • InterMine enables diverse data display and complex queries for TE reference sequences.

Conclusions:

  • RepetDB serves as a comprehensive TE knowledge base for de novo annotated genomes.
  • Facilitates exploration of TE families, superfamilies, and orders across species.
  • Enables cross-species searches and comparisons of TE family content.