Dfam 2.0 (September 2015, 4150 entries)
The Dfam database is a collection of Repetitive DNA element sequence alignments, hidden Markov models (HMMs) and matches lists for complete Eukaryote genomes. More...
Transposable elements (or interspersed repeats) account for a substantial portion of eukaryotic genomes. Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Dfam represents a collection of alignments and HMMs of such transposable elements and other repetitive DNA elements. The Dfam website gives information about each model, and provides genome annotations for a collection of core genomes. The models may also be downloaded from the ftp site, for example to mask repeats in new genomes.
You can find data in Dfam in various ways...
- Sequence Search
- View a Dfam Entry
- View a Sequence
- Keyword Search
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Or view the help pages for more information
Dfam_consensus is a related database of Repetitive DNA element sequence alignments and consensus sequence models. This open database provides family consensus models in a format that is compatible with an wide-variety of bioinformatics tools while facilitating the transition to Dfam style profile HMMs.
The Dfam database of repetitive DNA families
Robert Hubley; Robert D. Finn; Jody Clements; Sean R. Eddy; Thomas A. Jones; Weidong Bao; Arian F.A. Smit; Travis J. Wheeler
Nucleic Acids Research (2016) Database Issue 44:D81-89. doi: 10.1093/nar/gkv1272
Recent Dfam blog posts
Since its inception in 2012, Dfam has demonstrated the promise of using profile hidden Markov Models (HMMs) to improve the detection sensitivity and annotation quality of Transposable Element (TEs) families in human and subsequently for four additional reference organisms.Â Despite these advances, the tools used to discover new families ( de-novo repeat finders ), improve […]