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.


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 search against all Dfam models ( regardless of clade ) and using 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

Select an organism and enter a chromosome number and region, up to 50kbp (e.g. chr1:168180000-168130000).

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



Dfam_consensus

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.

Citing Dfam

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

Dfam project seeks postdoctoral fellow August, 2018

We are excited to announce the opening of a postdoctoral fellowship within the Dfam project and located at the Institute for Systems Biology (ISB) in Seattle. At ISB, the Smit lab is focused on the study of Transposable Element (TE) biology, and evolution using the latest developments in sequence modeling, phylogenetic reconstruction, and homology detection. We have developed […]