The Dfam database of repetitive DNA families

By Robert M. Hubley, Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Weidong Bao, Arian F. A. Smit, Travis J. Wheeler. Nucleic Acids Res., 2015

664 citations recorded by the source corpus.

Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/f780775b85986a2bf1d5849c56f621cb99efef3c

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Citations in the corpus

RepeatModeler2 for automated genomic discovery of transposable element families (2020, methodology): “Years of manual curation have resulted in high-quality consensus libraries for a limited set of species, mostly model organisms (19, 21, 22).”
RepeatModeler2: automated genomic discovery of transposable element families (2019, methodology): “RepeatModeler contains a basic homology-based classification module (RepeatClassifier) which compares the TE families generated by the various de novo tools to both the RepeatMasker Repeat Protein DB and to the RepeatMasker libraries (e.g. Dfam and/or RepBase).”
A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas (2020, neutral): “(Dfam Consensus-20170127 and RepBase-20170127) [70, 71] with parameters “-s -species “Crassostrea gigas” -e ncbi”.”
KRAB zinc finger proteins (2017, background): “However, because TEs become unrecognizable over time owing to mutational drift, it is likely that this represents an underestimate of their contribution to our genetic make-up (de Koning et al., 2011; Hubley et al., 2016).”