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Dfam specifications

Information


Unique identifier OMICS_03532
Name Dfam
Restrictions to use None
Database management system MySQL
Data access File download, Browse
Version 2.0
Maintained Yes

Maintainer


  • person_outline Dfam Team

Publications for Dfam

Dfam citations

 (42)
library_books

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High Throughput Sequencing for Novel Virus Detection

2018
PMCID: 5853486
PMID: 29564396
DOI: 10.1128/mSphereDirect.00069-18

[…] by using translated RefSeq viral genomic sequences (). To confirm the identity of retrotransposons, NHHMER was used to align nucleotide query sequences against profiles in the Repetitive DNA Element (DFAM) database v1.4 (). For BLASTX and PFAM analyses, DNA query sequences were translated to protein sequences in all six reading frames. Finally, nucleotide sequences without significant BLASTN hits […]

library_books

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

2018
PLoS One
PMCID: 5851578
PMID: 29538441
DOI: 10.1371/journal.pone.0193588

[…] programs: RepeatMasker, RepeatScout [], RECON [] and TRF (Tandem Repeat Finder) []. RepeatMasker identifies and masks interspersed repeats using curated libraries of consensus sequences supported by Dfam; Dfam contains entries corresponding to all Repbase TE entries, and each Dfam entry is represented by a profile hidden Markov model. RECON evaluates pair-wise similarities to build repeat consens […]

library_books

Ten steps to get started in Genome Assembly and Annotation

2018
F1000Res
PMCID: 5850084
PMID: 29568489
DOI: 10.5256/f1000research.14771.r31487

[…] e TEs . One of the best known is RepeatMasker, which harnesses nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher as search engines and uses curated libraries of repeats, currently supporting Dfam (profile HMM library) and Repbase , .Another important tool is the REPET package, one of the most used tools for large eukaryotic genomes with more than 50 genomes analyzed in the framework of in […]

library_books

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus

2017
BMC Evol Biol
PMCID: 5751776
PMID: 29297306
DOI: 10.1186/s12862-017-1103-z

[…] the AUGUSTUS package [] with the initial model “human” (H. sapiens) was used (Additional file ). The masking was performed with the RepeatMasker package [] using the RepBase repeats libraries [] and Dfam []. Annotation was carried out with scripts based on the funannotate pipeline [].The protein and transcriptomic hints for marking the position of genes were also used. Protein hints were obtained […]

library_books

A family based genome wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis

2017
PLoS One
PMCID: 5734761
PMID: 29253858
DOI: 10.1371/journal.pone.0185244

[…] the 406 individuals with nasal polyps, 350 were index patients with CRSwNP, 22 of the non-index patients knew they had polyps beforehand and 34 had newly discovered polyps.The Manhattan plot from the DFAM analysis is provided in and the Manhattan plot from the EMMAX analysis in . lists the 30 SNPs with the strongest associations from the DFAM analysis and lists the 30 SNPs with the strongest as […]

library_books

­­­Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia­­

2017
PMCID: 5674883
PMID: 28887438
DOI: 10.1083/jcb.201612160

[…] Consensus sequences for elements for up-regulated TEs were downloaded from the Dfam database (). Stranded RNA-seq data were then aligned to consensus sequences using BWA-MEM and quantified using HTseq-count (; ). Reads were visualized using the Integrative Genomics Viewer (IGV) […]

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Dfam institution(s)
Institute for Systems Biology, Seattle, WA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; HHMI Janelia Research Campus, Ashburn, VA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA; Genetic Information Research Institute, Los Altos, CA, USA; University of Montana, Missoula, MT, USA
Dfam funding source(s)
This work was supported by the Howard Hughes Medical Institute Janelia Research Campus and the National Institutes of Health [P41LM006252–1, RO1 HG002939]. The new Dfam database and web server was partially funded by a grant from the University of Montana University Grant Program.

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