Dfam 1.2 (May 2013, 1132 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.


Quick Links

You can find data in Dfam in various ways...

Sequence Search
Analyze your DNA sequence for Dfam matches

Paste your DNA sequence here to find matching Dfam entries.

This search will use the trusted cut-off thresholds (stringent). You can set your own search parameters here.

View a Dfam Entry
View Dfam entry annotation and alignments

Enter an entry identifier (e.g. AluJb) or accession (e.g. DF0000001) to see all data for that entry.

You can also browse through the list of all Dfam entries.

View a Sequence
View pre-calculated hits on a DNA sequence

Enter a chromosome number and region, up to 50kbp (e.g. 6/168180000-168130000).

At the moment, pre-calculated hits are only available for human.

Keyword Search
Query Dfam by keyword

Search for keywords in text data in the Dfam database.

You can also use the keyword search box at the top of every page.

Jump To
Go straight to the entry if you know the ID or accession

Enter any type of accession or ID to jump to the summary page for a Dfam entry.

Or view the help pages for more information


Citing Dfam

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 [...]