The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
Dfam: a database of repetitive DNA based on profile hidden Markov models
Open accessAbstract
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, built from alignments generated using RepeatMasker and Repbase. When used in conjunction with the hidden Markov model 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.
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Cites
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
The Pfam Protein Families Database
Bateman, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,000
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Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
Self-citationThe Pfam protein families database
Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1065 · Cited by 3,719
Self-citationBiological sequence analysis probabilistic models of proteins and nucleic acids
Durbin, R. M., Eddy, S. R., Krogh, A., & Mitchison, G. (1998) · Cited by 3,565
Self-citationRepbase Update, a database of eukaryotic repetitive elements
Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., & Walichiewicz, J. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084979 · Cited by 3,370
Self-citationBiological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
Durbin, R., Eddy, S. R., Krogh, A., & Mitchison, G. (1998) · Cambridge University Press eBooks · doi:10.1017/cbo9780511790492 · Cited by 3,246
Self-citationRepetitive Elements May Comprise Over Two-Thirds of the Human Genome
de Koning, A. P. J., Gu, W., Castoe, T. A., Batzer, M. A., & Pollock, D. D. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002384 · Cited by 1,112
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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-citationA comprehensive, cell specific microRNA catalogue of human peripheral blood.
Juzenas, S., Venkatesh, G., Hübenthal, M., Hoeppner, M. P., Du, Z. G., Paulsen, M., Rosenstiel, P., Senger, P., Hofmann-Apitius, M., Keller, A., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx706 · Cited by 181
A call for benchmarking transposable element annotation methods
Hoen, D. R., Hickey, G., Bourque, G., Casacuberta, J., Cordaux, R., Feschotte, C., Fiston-Lavier, A.-S., Hua-Van, A., Hubley, R., Kapusta, A., et al. (2015) · Mobile DNA · doi:10.1186/s13100-015-0044-6 · Cited by 105
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Metadata
- Authors
- Wheeler, T. J., Clements, J., Eddy, S. R., Hubley, R., Jones, T. A., Jurka, J., Smit, A. F. A., & Finn, R. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-11-30
- Volume
- 41
- Issue
- D1
- Pages
- D70-D82
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1969465720
- Cited by
- 306
- References
- 15
- FWCI
- 15.65
- Type
- journal article
- Language
- en
- Open access
- gold
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