The Dfam community resource of transposable element families, sequence models, and genome annotations

By Jessica M. Storer, Robert M. Hubley, Jeb Rosen, Travis J. Wheeler, Arian F. A. Smit. Mobile DNA, 2020

610 citations recorded by the source corpus.

Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam (https://dfam.org) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/a9a9279a78f012f45bf2917d988f765fcb4b63d4

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From telomere to telomere: the transcriptional and epigenetic state of human repeat elements (2021, background): “Despite this challenge, the expansion of a species-agnostic repeat database (Dfam)(7), extensive manual curation (e.”