RepetDB: a unified resource for transposable element references

• DOI: 10.1186/s13100-019-0150-y
• Publication Date: 2019-01-29T03:02:37Z
• Authors: Joëlle Amselem; Guillaume Cornut; Nathalie Choisne; Michael Alaux; Françoise Alfama-...; Véronique Jamilloux; Florian Maumus; Thomas Letellier; Isabelle Luyten; Cyril Pommier; Anne-Françoise Ad...; Hadi Quesneville
• Keywords: DNA Transposable Elements; Human genetics

Thanks to their ability move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors genome plasticity evolution. Their detection annotation considered essential in any sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements high-throughput technologies. A automated de novo process for TEs therefore required cope deluge sequence data. However, all procedures error-prone, an procedure TE identification classification would be no exception. It crucial provide not only reference sequences, but also evidence justifying classification, at scale whole genome. few databases already exist, none provides justify classification. Moreover, biological information about sequences remains globally poor. We present here RepetDB database developed framework GnpIS, a genetic genomic system. designed store retrieve detected, classified annotated standardized manner. implementation extensions InterMine, open-source data warehouse used store, search, browse, analyze compare recorded each sequence. InterMine can display diverse allows simple very complex queries. Finally, displayed via worldwide discovery portal. accessible urgi.versailles.inra.fr/repetdb . knowledge base populated full annotations complete (or near-complete) sequences. Indeed, description facilitates exploration specific families, superfamilies or orders across large range species. makes possible cross-species searches comparisons family content between genomes.