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Mobile Genetic Elements

Volume 859 of the series Methods in Molecular Biology pp 53-68

Date:

Roadmap for Annotating Transposable Elements in Eukaryote Genomes

  • Emmanuelle PermalAffiliated withUnité de Recherches en Génomique Info – URGI (UR1164) – INRA – Centre de Versailles
  • , Timothée FlutreAffiliated withUnité de Recherches en Génomique Info – URGI (UR1164) – INRA – Centre de Versailles
  • , Hadi QuesnevilleAffiliated withUnité de Recherches en Génomique Info – URGI (UR1164) – INRA – Centre de Versailles Email author 

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Abstract

Current high-throughput techniques have made it feasible to sequence even the genomes of non-model organisms. However, the annotation process now represents a bottleneck to genome analysis, especially when dealing with transposable elements (TE). Combined approaches, using both de novo and knowledge-based methods to detect TEs, are likely to produce reasonably comprehensive and sensitive results. This chapter provides a roadmap for researchers involved in genome projects to address this issue. At each step of the TE annotation process, from the identification of TE families to the annotation of TE copies, we outline the tools and good practices to be used.

Key words

Transposable elements Genome annotation Sequence analysis Bioinformatics Genomics