Dfam 1.1 (October 2012, 1143 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
TreeFam 9 is now available! May, 2013
We are happy to announce that TreeFam 9 is online and you can find it under http://www.treefam.org. TreeFam 9 now has 109 species (vs. 79 in TreeFam 8) and is based on data from Ensembl v69, Ensembl Genomes v16, Wormbase and JGI. This release marks an important step for TreeFam as it is the first [...]