The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
The Dfam database of repetitive DNA families
Open accessAbstract
Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download.
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
Cited by
RepeatModeler2 for automated genomic discovery of transposable element families
Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1921046117 · Cited by 3,848
Self-citationLiu, J., Dou, X., Chen, C., Chen, C., Liu, C., Xu, M. M., Zhao, S., Shen, B., Gao, Y., Han, D., et al. (2020) · Science · doi:10.1126/science.aay6018 · Cited by 709
Z-nucleic-acid sensing triggers ZBP1-dependent necroptosis and inflammation
Jiao, H., Wachsmuth, L., Kumari, S., Schwarzer, R., Lin, J., Eren, R. O., Fisher, A., Lane, R., Young, G. R., Kassiotis, G., et al. (2020) · Nature · doi:10.1038/s41586-020-2129-8 · Cited by 486
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements
Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., et al. (2022) · Science · doi:10.1126/science.abk3112 · Cited by 411
Self-citationMapping and phasing of structural variation in patient genomes using nanopore sequencing
Cretu Stancu, M., van Roosmalen, M. J., Renkens, I., Nieboer, M. M., Middelkamp, S., de Ligt, J., Pregno, G., Giachino, D., Mandrile, G., Espejo Valle-Inclan, J., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01343-4 · Cited by 404
Metadata
- Authors
- Hubley, R., Finn, R. D., Clements, J., Eddy, S. R., Jones, T. A., Bao, W., Smit, A. F. A., & Wheeler, T. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-26
- Volume
- 44
- Issue
- D1
- Pages
- D81-D89
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2226299262
- Cited by
- 784
- References
- 2
- FWCI
- 25.19
- Type
- journal article
- Language
- en
- Open access
- gold
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