____ __ | _ \ / _| __ _ _ __ ___ /\| | | |_ / _` | '_ ` _ \ \/|_| | _| (_| | | | | | | /\___/|_| \__,_|_| |_| |_| The Dfam community resource of transposable element families, sequence models, and genome annotations. RELEASE 3.9 ------------------------------------------------------------------------------- 1. INTRODUCTION Dfam is a collection of conserved DNA element sequence alignments, consensus sequences, hidden Markov models (HMMs) and complete genome annotations. Dfam contains curated libraries for five model organisms: Human, Mouse, Zebrafish, Worm and Fly as well as lineage-specific libraries for 242 mammals and a growing number of newly sequenced species. In addition, Dfam stores uncurated (de-novo produced) libraries for over 2000 additional species. 2. LOCATIONS Dfam is available on the web at: https://dfam.org/ 3. STATISTICS Dfam 3.9 consists of 4.1 million families across 2,784 taxa. Dfam families include retrotransposons, DNA transposons, interspersed repeats of unknown origin, and a number of non-TE entries used to annotate satellites or to avoid annotating noncoding RNA genes as TEs. The distribution of these constituent family types in each annotated species is given below: Curated Families (DF Records ) ------------------------------ Taxa Retrotransposons DNA Transposons Other ------- ---------------- --------------- ----- Mammalia 8864 1744 178 Sauropsida [Reptiles and Birds] 179 16 7 Actinopterygii [Bony Fishes] 1542 983 141 Insecta 1873 1079 3865 Viridiplantae [Green Plants] 262 38 0 Fungi 102 121 144 Other Metazoa 2064 1219 1856 Protists 3 0 0 Uncurated Families (DR Records ) -------------------------------- Taxa Retrotransposons DNA Transposons Other ------- ---------------- --------------- ----- Mammalia 196767 39701 24977 Sauropsida [Reptiles and Birds] 204695 70696 141229 Chondrichthyes [Cartilaginous Fishes] 13402 2031 11576 Actinopterygii [Bony Fishes] 190085 353219 333151 Petromyzontiformes [lampreys] 2876 997 1778 Amphibia 15165 12122 40181 Insecta 476393 404823 990684 Viridiplantae [Green Plants] 99892 51305 169184 Fungi 5935 3755 25758 Other Metazoa 36443 27095 122398 Protists 4360 2920 19525 4. CONSTRUCTION OF DFAM Dfam utilizes public genome assemblies and species-specific GARLIC [3] artificial benchmark sequences for each genome. Sequence alignments for the five model organisms were built using RepBase consensus sequences (http://www.girinst.org/repbase/) in a collaboration with GIRI. For these families the seed alignments were generated using RepeatMasker alignments of the consensus sequences against the current UCSC asssemblies (http://http://genome.ucsc.edu/ - hg38, ce10, dm6, mm10 and danRer10). For each family, annotated instances were transitively aligned based on mutual alignment to the Repbase consensus sequence. Hidden Markov models (HMMs) were constructed from the sequence alignment using the HMMER3 tool hmmbuild, and each model was then searched against Dfamseq using the HMMER3 tool nhmmer, with hit metadata (sequence location, score, etc) captured for distribution. As RepBase is a closed database, newer families in Dfam are based on seed alignments generated using additional methods including: directly from de-novo tools such as RepeatModeler and REPET, subfamily detection programs such as Coseg, and through manual clustering and alignment of genomic sequences. 5a. DESCRIPTION OF CHANGES FROM RELEASE 3.8 TO 3.9 Due to the recent interest and submission of libraries for Drosophila species, this release primarily focused on a thorough curation of the Dfam Drosophila melanogaster library. Special attention was given to reconciling families between Repbase, Flybase, and the Berkeley Drosophila Genome Project (BDGP) with new submissions from Gabriel Rech, Josefa Gonzales, and Sara Signor. This release also incorporates de novo libraries from two major initiatives: the Vertebrate Genomes Project and a eukaryote-wide study led by Landen Gozashti. Additionally, numerous individual genome and family submissions from the research community have been included. Library Submissions: - An updated Drosophila Melanogaster library representing detailed curation of new and existing families. This is the combined effort of Arian Smit, Clement Goubert, Gabriel Rech, Josefa Gonzales and Sara Signor. - 515 Eukaryote libraries provided by Landen Gozashti - 153 Vertebrate libraries provided by Hiram Clawson (UCSC, VGP) - Several highly curated primate families submitted by Martin Frith - Silverleaf Whitefly (Bemisia tabaci)library submitted by Juan Paolo Sicat - Atlantic Salmon (Salmo Salar) partial library submitted by Oystein Monsen - Waterlily Leafcutter Moth (Elophila obliteralis) submitted by Jacqueline Heckenhauer - The Gulf toadfish (Opsanus beta) submitted by Nicholas Kron - Castor Oil Plant (Ricinus communis) submitted by Kong Lin - Ascomycete Fungi (Zymoseptoria tritici) submitted by Tobias Baril - Oribatid Soil Mite (Oppia nitens) submitted by Derek Smith - Tanaka's Snailfish (Liparis Tanakae) submitted by Nathan Rives - SINES from 20 Bivalve species submitted by Jacopo Martelossi - Bengal Slow Loris (Nycticebus bengalensis) submitted by Charles Michie 5b. DESCRIPTION OF CHANGES FROM RELEASE 3.7 TO 3.8 The development of Dfam 3.8 was focused on two priorities, inclusion of a large set of community data submissions, and a refresh of the technology underpinning the website, API, and offline data formats. Library Submissions: - 71 plant genome libraries provided by Alexandre Paschoal - Walnut (Juglans mandshurica) library submitted by Chen Yidan - Coffee (Coffea eugenioides) submitted by Romain Guyot - Septoria linocola (fungal plant pathogen) library submitted by Adeline Simon - Deer Mouse (Peromyscus maniculatus) library submitted by Lande Gozashti - Eastern hap (Astatotilapia calliptera) library submitted by Pio Sierra - Stalk-eyed Fly (Teleopsis dalmanni) library submitted by Josephine Reinhardt - Libraries for 27 clam species submitted by Andrea Luchetti - 2 nematode libraries (Heligmosomoides bakeri and Heligmosomoides polygyrus) submitted by Isaac Martinez-Ugalde - Plasmodium falciparum (Protozoan parasite) library submitted by Samuel Ortion - Other updates and additions: HERV17 and related families by Martin Frith and Arian Smit Accession Length Changes: * Due to the fast growth of Dfam, we have found it necessary to increase the the Dfam accession number from 7-digits to 9-digits. Existing accessions have been converted by prefixing the existing accession with '00'. E.g DF0000001 becomes DF000000001. * The API, website, and export files (FamDB, HMMs, EMBL etc) have all been updated to the new accession format. Partitioned Data Export: * The FamDB HDF5 database format now supports database partitioning by taxonomic groups. This allows users to download only the portion(s) of Dfam that they need to conduct their work while still providing all the features the famdb.py query tool. At a minimum the root partition must be downloaded however any number of additional partitions may also be present. The files are available for downloaded from http://dfam.org/releases/Dfam_3.8/families/FamDB with the following taxonomic coverage: Partition 0 [dfam38_full.0.h5]: root Mammalia, Amoebozoa, Bacteria , Choanoflagellata, Rhodophyta, Haptista, Metamonada, Fungi, Sar, Placozoa, Ctenophora , Filasterea, Spiralia, Discoba, Cnidaria, Porifera, Viruses Partition 1 [dfam38_full.1.h5]: Obtectomera Partition 2 [dfam38_full.2.h5]: Euteleosteomorpha Partition 3 [dfam38_full.3.h5]: Sarcopterygii Sauropsida, Coelacanthimorpha, Amphibia, Dipnomorpha Partition 4 [dfam38_full.4.h5]: Diptera Partition 5 [dfam38_full.5.h5]: Viridiplantae Partition 6 [dfam38_full.6.h5]: Deuterostomia Chondrichthyes, Hemichordata, Cladistia, Holostei, Tunicata, Cephalochordata, Cyclostomata , Osteoglossocephala, Otomorpha, Elopocephalai, Echinodermata, Chondrostei Partition 7 [dfam38_full.7.h5]: Hymenoptera Partition 8 [dfam38_full.8.h5]: Ecdysozoa Nematoda, Gelechioidea, Yponomeutoidea, Incurvarioidea, Chelicerata, Collembola, Polyneoptera, Tineoidea, Apoditrysia, Monocondylia, Strepsiptera, Palaeoptera, Neuropterida, Crustacea, Coleoptera, Siphonaptera, Trichoptera, Paraneoptera, Myriapoda, Scalidophora This new format is compatible with the FamDB tools v1.0.1, and RepeatMasker 4.1.6. Dfam API and Website Improvements: * Several API endpoints have had their response times improved, most notably the `/families` endpoint. This is often queried for large amounts of data, so efficiency of the code has been priority. In this release, we have added a new caching system to handle large queries that would otherwise have timed out. In these cases the user may wait for the request to complete or come back at a later time to retrieve the results of the search. * The tech stack for Dfam.org was updated. The frontend was updated from Angular 11 to Angular 16 with the accompanying style changes. The API was migrated from Swagger to OpenAPI 3.0. 6. DESCRIPTION OF RELEASE FILES relnotes.txt - This file. userman.txt - A full description of Dfam data formats. families/ Dfam-#.hmm.gz - Dfam HMMs in an HMM library, searchable with the nhmmer program. Due to the large size, the file has been split into 10 files for easier downloading. Dfam-1.embl.gz - Dfam consensi in an EMBL library, searchable with the RepeatMasker 4.1.0 and earlier. Dfam-curated_only-1.hmm.gz - Dfam HMMs for curated (DF accessions only) families only. Dfam-curated_only-1.embl.gz - Dfam consensi for curated (DF accessions only) families in Dfam in EMBL format. families/FamDB/ dfam39_full.#.h5.gz - FamDB H5 partitions for use with the FamDB tool (https://github.com/Dfam-consortium/FamDB), and with RepeatMasker. This format stores the family HMMs, consensus sequences, and related taxonomy data in one file format, broken up by taxonomic groups. infrastructure/ dfamscan.pl - A basic search tool to query Dfam families against an input sequence. schema/ - Directory with printable ERD diagrams for Dfam apidocs/ - Dfam REST API documentation (HTML) 7. DESCRIPTION OF FIELDS See userman.txt for more detailed description of each field Compulsory fields: ------------------ AC Accession number: Accession number in form DFxxxxxxx. ID Identification: One word name for entry. DE Definition: Short description of entry. AU Author: Authors of the entry. SE Source of seed: The source suggesting the seed members belong to one entry. GA Gathering method: Score used for sequences within the clade specified by MS. TC Trusted Cutoff: Score used for sequences outside the clade specified by MS. NC Noise Cutoff: Smaller cutoff than GA; not used in Dfam. FR False Discovery Rate: Target FDR used to set GA. BM Build method SM Internal search method MS Model specificity: TaxID and TaxName, based on NCBI taxonomy. CT Classification tags: Repeat Type, Class, and Superfamily. SQ Sequence: Number of sequences in alignment. // End of alignment. Optional fields: ---------------- DC Database Comment: Comment about database reference. DR Database Reference: Reference to external database. RC Reference Comment: Comment about literature reference. RN Reference Number: Reference Number. RM Reference Medline: Eight digit medline UI number. RT Reference Title: Reference Title. RA Reference Author: Reference Author RL Reference Location: Journal location. PI Previous identifier: Record of all previous ID lines. CC Comment: Comments. WK Wikipedia Reference: Reference to wikipedia. SN Synonym A widely accepted alternative name for the model. CN Classification Note: A free text comment about the model classification. 8. REFERENCES 1. The Dfam Community Resource of Transposable Element Families, Sequence Models, and Genome Annotations. Storer, J., Hubley, R., Rosen, J., Wheeler, T., & Smit, A. F. Mobile DNA. 2021; 12: 2. https://doi.org/10.1186/s13100-020-00230-y 2. 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 44.D1 (2016): D81-D89. 3. Dfam: a Database of Repetitive DNA Based on Profile Hidden Markov Models Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AFA, Finn RD Nucl. Acids Res. (2013) Database Issue 41:D70-82. doi: 10.1093/nar/gks1265 4. Realistic artificial DNA sequences as negative controls for computational genomics. Caballero J, Smit AF, Hood L, Glusman G. Nucl. Acids Res. 2014 doi: 10.1093/nar/gku356 9. THE DFAM CONSORTIUM Dfam is maintained by a consortium of researchers. You can contact the Dfam consortium at: help@dfam.org The current/past members of the Dfam consortium are: Arian F. A. Smit, Robert Hubley, Anthony Gray: Institute for Systems Biology, USA Jessica Storer: University of Connecticut, USA Travis J. Wheeler, Clement Goubert, Jack Roddy: University of Arizona, USA Jeb Rosen: OneRail, USA Robert D. Finn: EBI, UK Jody Clements: Janelia Farm Research Campus, USA Sean R. Eddy, Thomas A. Jones: Harvard University, USA Jerzy Jurka: Genetic Information Research Institute, USA 11. ACKNOWLEDGEMENTS A.F.A.S., R.M.H., A.G., J.R. and T.J.W. were supported by a grant from the National Institutes of Health (NHGRI grant #U24-HG010136). R.D.F., J.C, S.R.E, T.A.J., and T.J.W received institutional support from HHMI Janelia Farm Research Campus. J.J. was supported by grants from the National Library of Medicine, National Institutes of Health (P41LM006252-12). A.F.A.S and R.H were supported by a grant from the National Institutes of Health (RO1 HG002939). 12. COPYRIGHT NOTICE Dfam - A database of conserved DNA element alignments and HMMs Copyright (C) 2015-2025 The Dfam consortium. This database is free; you can redistribute it and/or modify it as you wish, under the terms of the CC0 1.0 license, a 'no copyright' license: The Dfam consortium has dedicated the work to the public domain, waiving all rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. See Other Information below. Other Information o In no way are the patent or trademark rights of any person affected by CC0, nor are the rights that other persons may have in the work or in how the work is used, such as publicity or privacy rights. o Unless expressly stated otherwise, the Dfam consortium makes no warranties about the work, and disclaims liability for all uses of the work, to the fullest extent permitted by applicable law. o When using or citing the work, you should not imply endorsement by the Dfam consortium. You may also obtain a copy of the CC0 license here: http://creativecommons.org/publicdomain/zero/1.0/legalcode ___________________ The Dfam Consortium 2025