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Dfam

Dfam

Dfam is a web-based database containing transposable Element DNA sequence alignments (interspersed repeats), Hidden Markov Models (HMMs), consensus sequences, and genome annotations. The Dfam database represents the transposable element alignments as families together with annotations.

Topic

Sequence analysis; Sequence composition, complexity and repeats

Details

  • Operation: Data retrieval
  • Software interface: Web user interface
  • Language: -
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: CC0 1.0 Universal (CC0 1.0)
  • Cost: Free
  • Version name: 3.2
  • Maturity: Mature
  • Credit: The Howard Hughes Medical Institute Janelia Research Campus, the National Institutes of Health (NIH), the University of Montana University Grant Program
  • Contact: help _at_ dfam.org
  • Collection: -

Publications

Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ "The Dfam database of repetitive DNA families." Nucleic Acids Res, 2016 https://doi.org/10.1093/nar/gkv1272
PMID: 26612867
PMCID: PMC4702899


Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD "Dfam: a database of repetitive DNA based on profile hidden Markov models." Nucleic Acids Res, 2013 https://doi.org/10.1093/nar/gks1265
PMID: 23203985
PMCID: PMC3531169


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