Dfam 1.4 (May 2015, 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...
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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
Say hello to Dfam1.4 May, 2015
With Dfam, we are striving to build models of repeat families that yield high sensitivity without undue false annotation. In thisrelease of Dfam, we have improved our model building strategy toreduce the potential for false annotation, especially in the contextof overextending alignments around true interspersed repeat instances. A new benchmark for False Positives, Using GARLIC In […]