Dfam
Names
More detailed information about this field from each metasource.
Dfam
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
dfam
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
Names
More detailed information about this field from each metasource.
Dfam
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
dfam
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
Names
More detailed information about this field from each metasource.
Dfam
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
dfam
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
The Dfam database is a open collection of DNA Transposable Element sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. Dfam represents a collection of multiple sequence alignments, each containing a set of representative members of a specific transposable element family. These alignments (seed alignments) are used to generate HMMs and consensus sequences for each family. The Dfam website gives information about each family, and provides genome annotations for a collection of core genomes.
Description
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The Dfam database is a open collection of DNA Transposable Element sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. Dfam represents a collection of multiple sequence alignments, each containing a set of representative members of a specific transposable element family. These alignments (seed alignments) are used to generate HMMs and consensus sequences for each family. The Dfam website gives information about each family, and provides genome annotations for a collection of core genomes.
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which is made up of remnants of transposable elements (TEs). Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Identification and masking of TEs can also greatly simplify many downstream genome annotation and sequence analysis tasks. The commonly-used TE annotation tools RepeatMasker and Censor depend on sequence homology search tools such as cross_match and BLAST variants, as well as Repbase, a collection of known TE families each represented by a single consensus sequence. Dfam contains entries corresponding to all Repbase TE entries for which instances have been found in the human genome. Each Dfam entry is represented by a profile hidden Markov model (HMM), built from alignments generated using RepeatMasker and Repbase. When used in conjunction with the HMM search tool nhmmer, Dfam produces a 2.9% increase in coverage over consensus-sequence search methods on a large human benchmark, while maintaining low false discovery rates, and coverage of the full human genome is 54.5%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The Dfam database is a open collection of Transposable Element DNA sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
Webpage:
http://dfam.org/Webpage
More detailed information about this field from each metasource.
http://dfam.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
https://dfam.org
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
Licence:
Name: Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain DedicationLicence name
More detailed information about this field from each metasource.
Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
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https://creativecommons.org/publicdomain/zero/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
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The Dfam database of repetitive DNA families
PMID: 26612867
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gks1265
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.21203/RS.3.RS-76062/V1
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
Publications
More detailed information about this field from each metasource.
The Dfam database of repetitive DNA families
PMID: 26612867
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gks1265
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.21203/RS.3.RS-76062/V1
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
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The Dfam database of repetitive DNA families
PubMed citations: 230.
230 articles citing: The Dfam database of repetitive DNA families
Influenza A Virus Infection Reactivates Human Endogenous Retroviruses Associated with Modulation of Antiviral Immunity. PMID:35891571
Comparative Analysis of the pIgR Gene from the Antarctic Teleost Trematomus bernacchii Reveals Distinctive Features of Cold-Adapted Notothenioidei. PMID:35887127
Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1. PMID:35789859
The genome of Prunus humilis provides new insights to drought adaption and population diversity. PMID:35751601
Comprehensive In Silico Analysis of Retrotransposon Insertions within the Survival Motor Neuron Genes Involved in Spinal Muscular Atrophy. PMID:35741345
Functional characterization of piggyBac-like elements from Nilaparvata lugens (Stål) (Hemiptera: Delphacidae). PMID:35686529
Chromosome-Scale, Haplotype-Resolved Genome Assembly of Suaeda Glauca. PMID:35646071
Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes. PMID:35637228
The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology. PMID:35628657
Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea. PMID:35627288
Mobilome of Apicomplexa Parasites. PMID:35627271
Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families. PMID:35591887
A Genome for Bidens hawaiensis: A Member of a Hexaploid Hawaiian Plant Adaptive Radiation. PMID:35575077
Reconstruction of full-length LINE-1 progenitors from ancestral genomes. PMID:35552404
Software evaluation for de novo detection of transposons. PMID:35477485
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment. PMID:35469019
Testicular "Inherited Metabolic Memory" of Ancestral High-Fat Diet Is Associated with Sperm sncRNA Content. PMID:35453658
A Chromosome-Scale Hybrid Genome Assembly of the Extinct Tasmanian Tiger (Thylacinus cynocephalus). PMID:35349647
Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements. PMID:35348724
The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome. PMID:35348678
Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics. PMID:35348662
Chromosome length genome assembly of the redbanded stink bug, Piezodorus guildinii (Westwood). PMID:35317820
Chromosomal-Level Genome Assembly of the Springtail Tomocerus qinae (Collembola: Tomoceridae). PMID:35298623
Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus. PMID:35172896
Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut. PMID:35134055
Target Gene Diversity of the Nrf1-MafG Transcription Factor Revealed by a Tethered Heterodimer. PMID:35129372
The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma. PMID:35118386
A Chromosome-Level Genome Assembly of the Parasitic Wasp Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae). PMID:35104339
Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. PMID:35075135
In silico analysis of potential off-target sites to gene editing for Mucopolysaccharidosis type I using the CRISPR/Cas9 system: Implications for population-specific treatments. PMID:35073349
Prediction and analysis of functional RNA structures within the integrative genomics viewer. PMID:35047817
Finding and Characterizing Repeats in Plant Genomes. PMID:35037215
Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map. PMID:35022701
PlantRep: a database of plant repetitive elements. PMID:34977976
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). PMID:34927191
msRepDB: a comprehensive repetitive sequence database of over 80 000 species. PMID:34850956
Identification and Characterization of New Alu Element Insertion in the BRCA1 Exon 14 Associated with Hereditary Breast and Ovarian Cancer. PMID:34828342
Genome Survey Sequencing of an Iconic 'Trophy' Sportfish, the Roosterfish Nematistius pectoralis: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery. PMID:34828317
Identification of differentially expressed genomic repeats in primary hepatocellular carcinoma and their potential links to biological processes and survival. PMID:34803457
AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes. PMID:34792587
Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation. PMID:34764282
Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes. PMID:34758315
DNA methylation profile in patients with indolent systemic mastocytosis. PMID:34754417
Sex without crossing over in the yeast Saccharomycodes ludwigii. PMID:34732243
Transposable elements that have recently been mobile in the human genome. PMID:34732136
Sperm epigenetic alterations contribute to inter- and transgenerational effects of paternal exposure to long-term psychological stress via evading offspring embryonic reprogramming. PMID:34711814
DREAM represses distinct targets by cooperating with different THAP domain proteins. PMID:34686342
Chromosome-Level Genome Assembly of Nephotettix cincticeps (Uhler, 1896) (Hemiptera: Cicadellidae: Deltocephalinae). PMID:34677607
Sequence features of retrotransposons allow for epigenetic variability. PMID:34668484
Chromosome-Level Genome Assembly and Annotation of the Fiber Flax (Linum usitatissimum) Genome. PMID:34589116
A prenylated dsRNA sensor protects against severe COVID-19. PMID:34581622
Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans. PMID:34506495
High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing. PMID:34488624
Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer. PMID:34479546
The whale shark genome reveals patterns of vertebrate gene family evolution. PMID:34409936
Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain. PMID:34400477
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells. PMID:34390351
Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti). PMID:34370317
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. PMID:34341414
Endogenous Retroviruses Drive Lineage-Specific Regulatory Evolution across Primate and Rodent Placentae. PMID:34320657
Highly contiguous assemblies of 101 drosophilid genomes. PMID:34279216
Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus). PMID:34270728
Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm. PMID:34252082
Diploidy within a Haploid Genus of Entomopathogenic Fungi. PMID:34247231
Evolution of mouse circadian enhancers from transposable elements. PMID:34187518
A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues. PMID:34172835
Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. PMID:34140313
Curation Guidelines for de novo Generated Transposable Element Families. PMID:34138525
Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region. PMID:34122517
Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome. PMID:34070911
HERV-K(HML7) Integrations in the Human Genome: Comprehensive Characterization and Comparative Analysis in Non-Human Primates. PMID:34069102
The Worldwide Invasion of Drosophila suzukii Is Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions. PMID:34021759
A Chromosome-Level Genome Assembly of Ephestia elutella (Hübner, 1796) (Lepidoptera: Pyralidae). PMID:34014321
A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon. PMID:33986770
Disentangling the aging gene expression network of termite queens. PMID:33975542
The Transposable Elements of the Drosophila serrata Reference Panel. PMID:33950180
Universal nomenclature for oxytocin-vasotocin ligand and receptor families. PMID:33911268
Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species. PMID:33772558
A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas. PMID:33764468
Nanopore Sequencing Indicates That Tandem Amplification of Chromosome 20q11.21 in Human Pluripotent Stem Cells Is Driven by Break-Induced Replication. PMID:33757297
The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. PMID:33750380
Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes. PMID:33747544
A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.). PMID:33734373
aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin. PMID:33693861
Long-read sequencing and de novo genome assemblies reveal complex chromosome end structures caused by telomere dysfunction at the single nucleotide level. PMID:33693840
Genomic properties of variably methylated retrotransposons in mouse. PMID:33612119
Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type. PMID:33598705
A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes. PMID:33561231
Draft genome sequence, annotation, and SSR mining data of Elaeidobius kamerunicus Faust., an essential oil palm pollinating weevil. PMID:33537371
SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction. PMID:33537058
Search for SINE repeats in the rice genome using correlation-based position weight matrices. PMID:33530928
A Highly Contiguous Genome Assembly of a Polyphagous Predatory Mite Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae). PMID:33528489
A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing. PMID:33501937
Transposable element subfamily annotation has a reproducibility problem. PMID:33485368
Phylogenomics of the Maverick Virus-Like Mobile Genetic Elements of Vertebrates. PMID:33481003
Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus. PMID:33479356
The Dfam community resource of transposable element families, sequence models, and genome annotations. PMID:33436076
Selfing is the safest sex for Caenorhabditis tropicalis. PMID:33427200
Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence. PMID:33402863
TFs for TEs: the transcription factor repertoire of mammalian transposable elements. PMID:33397727
Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery. PMID:33362980
Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics. PMID:33352976
Argonaute NRDE-3 and MBT domain protein LIN-61 redundantly recruit an H3K9me3 HMT to prevent embryonic lethality and transposon expression. PMID:33303642
Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation. PMID:33287227
Massively multiplex single-molecule oligonucleosome footprinting. PMID:33263279
Draft Genome Sequence of Oleaginous Yeast Saitozyma sp. Strain JCM 24511, Isolated from Soil on Iriomote Island, Okinawa, Japan. PMID:33239459
Genome-wide discovery and characterization of long noncoding RNAs in African oil palm (Elaeis guineensis Jacq.). PMID:33194332
Towards a better understanding of the low recall of insertion variants with short-read based variant callers. PMID:33148192
Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option. PMID:33077915
Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. PMID:33020268
A Novel Microduplication Spanning Exons 8-16 of ATP2C1 That Was Undetectable by Standard Sanger Sequencing in a Japanese Patient With Hailey-Hailey Disease. PMID:33015087
Tissue-specific usage of transposable element-derived promoters in mouse development. PMID:32988383
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Unusually efficient CUG initiation of an overlapping reading frame in POLG mRNA yields novel protein POLGARF. PMID:32958672
PacBio genome sequencing reveals new insights into the genomic organisation of the multi-copy ToxB gene of the wheat fungal pathogen Pyrenophora tritici-repentis. PMID:32957933
Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods. PMID:32947622
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing. PMID:32917720
Endogenous retroviruses drive species-specific germline transcriptomes in mammals. PMID:32895553
Daxx maintains endogenous retroviral silencing and restricts cellular plasticity in vivo. PMID:32821827
Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. PMID:32821405
A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. PMID:32808665
Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency. PMID:32795400
A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore. PMID:32722451
An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs. PMID:32697302
Machine Boss: rapid prototyping of bioinformatic automata. PMID:32683444
Genetic Diversity in Invasive Populations of Argentine Stem Weevil Associated with Adaptation to Biocontrol. PMID:32674400
RNA-Seq Transcriptome Analysis Reveals Long Terminal Repeat Retrotransposon Modulation in Human Peripheral Blood Mononuclear Cells after In Vivo Lipopolysaccharide Injection. PMID:32669333
Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia. PMID:32665538
Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data. PMID:32662945
Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates. PMID:32602886
Measuring and interpreting transposable element expression. PMID:32576954
Effects of Mutations in the Drosophila melanogaster Rif1 Gene on the Replication and Underreplication of Pericentromeric Heterochromatin in Salivary Gland Polytene Chromosomes. PMID:32575592
Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight. PMID:32546503
An improved pig reference genome sequence to enable pig genetics and genomics research. PMID:32543654
Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy. PMID:32527930
DNA steganography: hiding undetectable secret messages within the single nucleotide polymorphisms of a genome and detecting mutation-induced errors. PMID:32527315
Repetitive DNA profile of the amphibian mitogenome. PMID:32429835
Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance. PMID:32423419
The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes). PMID:32386319
Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master's Course. PMID:32385046
Genomic competition for noise reduction shaped evolutionary landscape of mir-4673. PMID:32376854
Independent Whole-Genome Duplications Define the Architecture of the Genomes of the Devastating West African Cacao Black Pod Pathogen Phytophthora megakarya and Its Close Relative Phytophthora palmivora. PMID:32354704
Comprehensive Analysis of HERV Transcriptome in HIV+ Cells: Absence of HML2 Activation and General Downregulation of Individual HERV Loci. PMID:32340287
RepeatModeler2 for automated genomic discovery of transposable element families. PMID:32300014
Z-nucleic-acid sensing triggers ZBP1-dependent necroptosis and inflammation. PMID:32296175
Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. PMID:32286261
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. PMID:32266012
Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage. PMID:32219172
Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers. PMID:32193341
Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding. PMID:32162128
Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization. PMID:32111628
Activation of Transposable Elements in Immune Cells of Fibromyalgia Patients. PMID:32085571
Mobile genomics: tools and techniques for tackling transposons. PMID:32075565
Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild. PMID:32055408
Virus-induced transposable element expression up-regulation in human and mouse host cells. PMID:31964680
Epigenetic therapy of myelodysplastic syndromes connects to cellular differentiation independently of endogenous retroelement derepression. PMID:31870430
A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans. PMID:31827084
Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. PMID:31825311
Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene. PMID:31817529
Specific trophoblast transcripts transferred by extracellular vesicles affect gene expression in endometrial epithelial cells and may have a role in embryo-maternal crosstalk. PMID:31727082
DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double-stranded RNA foci in human cell models of FSHD. PMID:31630170
The genome of Populus alba x Populus tremula var. glandulosa clone 84K. PMID:31580414
AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. PMID:31360240
Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants. PMID:31316532
Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes. PMID:31304534
Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids. PMID:31293619
ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation. PMID:31284879
Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths. PMID:31214686
Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development. PMID:31182756
Comprehensive Characterization of the Human Endogenous Retrovirus HERV-K(HML-6) Group: Overview of Structure, Phylogeny, and Contribution to the Human Genome. PMID:31167914
Interspecies conservation of organisation and function between nonhomologous regional centromeres. PMID:31138803
A haplotype-resolved draft genome of the European sardine (Sardina pilchardus). PMID:31112613
Human contamination in bacterial genomes has created thousands of spurious proteins. PMID:31064768
DNA methylome of human neonatal umbilical cord: Enrichment of differentially methylated regions compared to umbilical cord blood DNA at transcription factor genes involved in body patterning and effects of maternal folate deficiency or children's sex. PMID:31063509
Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines. PMID:31061680
DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition. PMID:31056858
Transposable elements drive widespread expression of oncogenes in human cancers. PMID:30926969
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. PMID:30902113
Long live the queen, the king and the commoner? Transcript expression differences between old and young in the termite Cryptotermes secundus. PMID:30759161
RepetDB: a unified resource for transposable element references. PMID:30719103
A High-quality Draft Genome Assembly of Sinella curviseta: A Soil Model Organism (Collembola). PMID:30668671
Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. PMID:30626321
Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses. PMID:30587213
Variation in proviral content among human genomes mediated by LTR recombination. PMID:30568734
ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses. PMID:30455304
AFLP-AFLP in silico-NGS approach reveals polymorphisms in repetitive elements in the malignant genome. PMID:30408048
Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles. PMID:30372484
Statistical modelling of CG interdistance across multiple organisms. PMID:30367587
Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing. PMID:30355765
CAGm: a repository of germline microsatellite variations in the 1000 genomes project. PMID:30329086
Draft genome assembly of the invasive cane toad, Rhinella marina. PMID:30101298
De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations. PMID:30072691
Fern genomes elucidate land plant evolution and cyanobacterial symbioses. PMID:29967517
IsopiRBank: a research resource for tracking piRNA isoforms. PMID:29961820
Tau Activates Transposable Elements in Alzheimer's Disease. PMID:29874575
Longevity and transposon defense, the case of termite reproductives. PMID:29735660
A family of long intergenic non-coding RNA genes in human chromosomal region 22q11.2 carry a DNA translocation breakpoint/AT-rich sequence. PMID:29668722
The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. PMID:29601845
A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection. PMID:29564396
Repressive Chromatin in Caenorhabditis elegans: Establishment, Composition, and Function. PMID:29378810
Physiological and Pathological Transcriptional Activation of Endogenous Retroelements Assessed by RNA-Sequencing of B Lymphocytes. PMID:29312197
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. PMID:29297306
Alu element insertion in PKLR gene as a novel cause of pyruvate kinase deficiency in Middle Eastern patients. PMID:29288557
Loss of p53-inducible long non-coding RNA LINC01021 increases chemosensitivity. PMID:29262524
Cut-and-Paste Transposons in Fungi with Diverse Lifestyles. PMID:29228286
Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories. PMID:29225705
Living Organisms Author Their Read-Write Genomes in Evolution. PMID:29211049
A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition. PMID:29165679
Identification of a novel HERV-K(HML10): comprehensive characterization and comparative analysis in non-human primates provide insights about HML10 proviruses structure and diffusion. PMID:29118853
Mapping and phasing of structural variation in patient genomes using nanopore sequencing. PMID:29109544
Highly sensitive and specific Alu-based quantification of human cells among rodent cells. PMID:29038571
Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia. PMID:28887438
De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. PMID:28873963
Transposable elements are the primary source of novelty in primate gene regulation. PMID:28855262
Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens. PMID:28801508
Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PMID:28749982
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. PMID:28746312
Associating transcription factors and conserved RNA structures with gene regulation in the human brain. PMID:28720872
Genome annotation for clinical genomic diagnostics: strengths and weaknesses. PMID:28558813
A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. PMID:28532419
Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. PMID:28522611
Nucleosome repositioning during differentiation of a human myeloid leukemia cell line. PMID:28406749
Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition. PMID:28323615
A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress. PMID:28294943
The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine? PMID:28090383
Genome-wide mapping of autonomous promoter activity in human cells. PMID:28024146
The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation. PMID:27980690
Endogenous retroviral promoter exaptation in human cancer. PMID:27980689
Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes. PMID:27791097
CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome. PMID:27402545 - http://dx.doi.org/10.1093/nar/gks1265
- http://dx.doi.org/10.21203/RS.3.RS-76062/V1
Tags:
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
hidden markov model
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
multiple sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
transposable element
metasource: Fairsharing.org
version: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
coding and non-coding dna
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
dna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
phylogeny
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
mobile genetic elements
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
sequence assembly
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
plant biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:58.786784
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
dna sequence data
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
hidden markov model
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
multiple sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
transposable element
metasource: Fairsharing.orgversion: FAIRsharing.org: Dfam; Dfam; DOI: https://doi.org/10.25504/FAIRsharing.6ktmmc; Last edited: Feb. 25, 2020, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
coding and non-coding dna
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
dna
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
phylogeny
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
mobile genetic elements
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
sequence assembly
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
plant biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:58.786784
dna sequences genome genome annotation hidden markov model multiple sequence alignment transposable element nucleic acid sequence coding and non-coding dna dna phylogeny mobile genetic elements sequence assembly plant biology
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