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Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9. doi: 10.1093/nar/gkv1272. Epub 2015 Nov 26.

The Dfam database of repetitive DNA families.

Author information

1
Institute for Systems Biology, Seattle, WA 98109, USA rhubley@systemsbiology.org.
2
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1RQ, UK.
3
HHMI Janelia Research Campus, Ashburn, VA 20147, USA.
4
Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
5
Genetic Information Research Institute, Los Altos, CA 94022, USA.
6
Institute for Systems Biology, Seattle, WA 98109, USA.
7
University of Montana, Missoula, MT 59812, USA travis.wheeler@umontana.edu.

Abstract

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.

PMID:
26612867
PMCID:
PMC4702899
DOI:
10.1093/nar/gkv1272
[Indexed for MEDLINE]
Free PMC Article

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