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

Introducing Dfam_consensus – Dfam’s consensus sequence twin May, 2017

Since its inception in 2012, Dfam has demonstrated the promise of using profile hidden Markov Models (HMMs) to improve the detection sensitivity and annotation quality of Transposable Element (TEs) families in human[1] and subsequently for four additional reference organisms[2].  Despite these advances, the tools used to discover new families ( de-novo repeat finders ), improve […]