Dfam is an open access database of transposable element (TE) and DNA satellite families, organized around multiple sequence alignments of representative family members ("seed alignments") and their derived consensus and profile hidden Markov models (pHMMs). The initial versions of the database contained meticulously curated transposable element (TE) families and annotations tailored to a select group of model organisms [1,2]. Recently, it has undergone significant expansion to accommodate the storage and analysis of a vast array of de novo TE libraries, enhancing its capacity for comprehensive research and exploration. The latest release of Dfam (3.8) has returned the focus to curated libraries contributed by the community with the inclusion of 101 new species libraries, as well as updates to the technologies underpinning the website and API. Moreover, in response to the rapid growth of the database, the FamDB export format has been refactored to support partial downloads of the database partitioned by taxonomic groups. Dfam currently hosts an extensive collection of 3.6 million TE families spanning over 2,437 taxa, and we look forward to its further expansion with your help.
1 Wheeler, Travis J., et al. "Dfam: a database of repetitive DNA based on profile hidden Markov models." Nucleic acids research 2012.
2 Hubley, Robert, et al. “The Dfam database of repetitive DNA families.” Nucleic Acids Research 2016
| Subject : | : | poster |
| Topics | : | Education and outreach (poster only) |
| Keywords | : | Dfam ; Database ; Community Resource ; pHMM ; models ; API ; TE ; de novo ; curation |
| PDF version | : |  PDF version |
