Dfam: a database of repetitive DNA based on profile hidden Markov models

By Travis J. Wheeler, Jody Clements, Sean R. Eddy, Robert M. Hubley, Thomas A. Jones, Jerzy Jurka, Arian F. A. Smit, Robert D. Finn. Nucleic Acids Res., 2012

297 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/e14863d8a594f622f0b5c84e9f220720e398a5b5

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Citations in the corpus

Repbase Update, a database of repetitive elements in eukaryotic genomes (2015, methodology): “In addition to Repeat-Masker, RU is also essential for the Dfam database [18], where the profile hidden Markov models (profile HMMs) for different repeats are used in conjunction with the HMM search tool nhmmer to detect repetitive sequences in the genome [18].”
The Dfam database of repetitive DNA families (2015, methodology): “Similar indications of overextension (not shown) were seen in a benchmark with design much like that in (17), but where repeat copies were placed in reversed sequence in precisely the same position in which they occurred in unreversed sequence (i.”
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models (2014, methodology): “Skylign ’ s interactive logos are easily incorporated into a web page, and we have already used them in our HMMER and Dfam webservers, presenting logos for both protein and DNA profile HMMs [10,27].”