DFAM : Multiple alignment, consensus sequences, and profile HMMs of repetitive DNA RELEASE 3.2 -------------------------------------- 1. INTRODUCTION Dfam is a collection of conserved DNA element sequence alignments, consensus sequences, hidden Markov models (HMMs) and complete genome annotations. Dfam has full, curated libraries for five model organisms: Human, Mouse, Zebrafish, Worm and Fly as well as curated libraries for a growing number of newly sequenced species. In addition, Dfam now stores uncurated ( de-novo produced ) families for over 336 additional species. 2. LOCATIONS Dfam is available on the web at: https://dfam.org/ 3. STATISTICS Dfam 3.2 consists of 273,655 families across 347 species. 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 ) ------------------------------- Species Retrotransposons DNA Transposons Other ------- ---------------- --------------- ----- Human 824 334 149 Mouse 941 297 133 C. Elegans 58 100 29 D. Melanogaster 165 27 21 Danio Rerio 1077 769 118 Cape Golden Mole 365 288 122 Painted Turtle* 62 72 103 Collard Flycatcher 121 57 110 Brown Marmorated Stink Bug 373 209 1366 Blue-capped cordon-bleu 103 57 103 Postman Butterfly 307 308 6 Red Postman Butterfly 307 308 6 * partial library. Uncurated Families (DR Records ) -------------------------------- Taxa Retrotransposons DNA Transposons Other ------- ---------------- --------------- ----- Mammalia 18301 3781 2567 Sauropsida [Lizards and Birds] 29326 11688 27192 Amphibia 1781 2031 6107 Actinopterygii [Bony Fishes] 27520 51361 77006 Chondrichthyes [Cartilaginous Fishes] 1671 198 2273 Viridiplantae [Green Plants] 896 412 1687 4. CONSTRUCTION OF DFAM Dfam utilizes public genome assemblies to produce family annotation results. This release of Dfam contains annotations on the following assemblies: H. sapiens ( GRCh38 ), C. elegans ( ce10 ), D. melanogaster ( dm6 ), M. musculus ( mm10 ), D. rerio ( danRer10 ), C. asiatica ( chrAsi1 ), C. picta bellii ( chrPic2 ), H. halys ( halHal1 ), F. albicollis ( ficAlb2 ), U. cyanocephalus ( DAuraCya0.8 ), H. melpomene melpomene ( DAhelMel2.5 ), and H. erato demophoon ( DAhelEra1 ) 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. 5. DESCRIPTION OF CHANGES FROM RELEASE 3.1 to 3.2 Support for Uncurated Families: * Uncurated families are families that have been generated using any number of de-novo TE discovery methods on newly assembled genomes. These families have not received any significant curation effort and likely contain some amount of non-TE content ( gene families, satellites etc ). In addition these families are often redundant between species ( ancestral to the species it was identified in ) or even within the species ( due to cryptic subfamily structure, deletion products etc ). Finally these families tend to be heavily fragmented. The uncurated families are designated with a 'DR' accession prefix. * Each of these families includes a seed alignment, a profile HMM, and a model synchronized consensus sequence. Unlike curated families, DR records have not been rigorously thresholded and full genome annotations are not provided. Relationships to other families and TE protein similarity have been generated to facilitate curation efforts on these families. EBI RepeatModeler Dataset: * In collaboration with the Fergal Martin, and Denye Ogeh at the European Bioinformatics Institute we processed and imported RepeatModeler runs on 336 species ( 266,740 families ). This massive dataset will provide immediate functionality for use in assembly masking and over time as starting point for curation efforts in these species. Website Improvements: * Numerous changes to the Family view have been made to accomodate the new 'DR' uncurated families. * In addition to curated protein annotations for each family, Dfam now provides BLASTX alignments for each family to the RepeatMasker TE protein database. * Families identified using a search on the Browse bage may now be downloaded as a single HMM, EMBL or FASTA file. * A new dataset of common DNA Transposon termini patterns may now be found on the Classification page. * The seed alignment Kimura divergence is now displayed on the Seed tab of each family. 6. DESCRIPTION OF RELEASE FILES relnotes.txt - This file. userman.txt - A fuller description of Dfam fields. families/ Dfam.hmm.gz - Dfam HMMs in an HMM library, searchable with the nhmmer program. Dfam.embl.gz - Dfam consensi in an EMBL library, searchable with the RepeatMasker program. Dfam.curatedonly.hmm.gz - Dfam HMMs for curated (DF accessions only) families only. Dfam.curatedonly.embl.gz - Dfam consensi for curated (DF accessions only) families in Dfam in EMBL format. annotations// _dfam.hits - TSV list of all matches found in the given assembly that score above the GA threshold. ie. hg38_dfam.hits.gz _dfam.nrph.hits - TSV list of all non-redundant matches found in the given assembly and that score above the GA threshold. ie. hg38_dfam.nrph.hits.gz infrastructure/ dfamscan.pl - A basic search tool to query Dfam families against an input sequence. schema/ - Directory with printable ERD diagrams for Dfam db-exports/ - A full export of the mysql database 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 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 Nucl. Acids Res. In Press. 2. 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 3. 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, Jessica Storer and Jeb Rosen: Institute for Systems Biology, USA Travis J. Wheeler: University of Montana, USA Robert D. Finn: EMBL, 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., 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) 2015-2020 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. 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