Dfam 1.3 (December 2014, 1306 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: a database of repetitive DNA based on profile hidden Markov models
Travis J. Wheeler; Jody Clements; Sean R. Eddy; Robert Hubley; Thomas A. Jones; Jerzy Jurka; Arian F. A. Smit; Robert D. Finn
Nucleic Acids Research (2013) Database Issue 41:D70-82. doi: 10.1093/nar/gks1265
Recent Dfam blog posts
Dfam 1.3 released January, 2015
We are pleased to announce the release of Dfam 1.3. This release includes almost 200 new repeat families and updates the underlying human genome to hg38. New families, new seeds, new genome We’ve added 185 new repeat families found in the human genome. Seed alignments for all families have been updated with an improved construction script, using only hg38 sequences. New […]