DFAM : Multiple alignment, consensus sequences, and profile HMMs of repetitive DNA RELEASE 3.0 -------------------------------------- 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 libraries for five model organisms: Human, Mouse, Zebrafish, Worm and Fly as well as partial libraries for four additional species. 2. LOCATIONS Dfam is available on the web at: https://dfam.org/ 3. STATISTICS Dfam 3.0 consists of 6235 models. 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: 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 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 ), and F. albicollis ( ficAlb2 ) 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 2.0 to 3.0 1. Dfam and Dfam_consensus have been merged into one comprehensive database for transposable element family consensus sequences and profile Hidden Markov Models. Consensus sequences were generated using the seed alignment data for each family. These sequences may differ from RepBase and in many cases reflect an improvement owing to deeper seed alignments that they are called from. The consensus sequences appear in the model tab of each family and an EMBL file download link is provided. The complete set of consensi for Dfam is also included in the families directory of this release. 2. The website and underlying database schema were refactored to facilitate future growth of the database. The development of a Dfam REST API is a product of this refactoring and provides new functionality for Dfam. The API provides a means for users to programatically obtain data directly from the database. Full documentation on this new feature is available under the help page of the website. 3. The Repeat Protein Database ( a product distributed with RepeatMasker ) has now been integrated into Dfam. The new 'Features' tab in the family view displays coding region details for families that have entries in this protein database. 4. The seed alignment visualization that was part of Dfam_consensus is now incorporated into Dfam. This visualization combines the coverage and whisker plots into one visualization. In addition, using a heatmap approach the whisker plot displays the quality of subregions in the alignment. 5. The new transposable element classification system in Dfam_consensus was adopted for Dfam. See the 'Classification' section of the website for further details. 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.seed.gz - Deprecated. This dataset is available in the infrastructure/db-exports/seed_region MySQL table file in this and future releases. Individual family Stockholm files are available through the website and throught the API. 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, 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. 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