title: Roadmap for annotating transposable elements in eukaryote genomes.
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.
authors.affiliation: Unité de Recherches en Génomique Info - URGI (UR1164) - INRA - Centre de Versailles, Versailles cedex, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Permal
authors.forename: Timothée
authors.initials: T
authors.lastname: Flutre
authors.forename: Hadi
authors.initials: H
authors.lastname: Quesneville
mesh_terms: D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D004251:DNA Transposable Elements / Q000235:genetics*; D056890:Eukaryota / Q000235:genetics*; D016678:Genome; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004251:DNA Transposable Elements