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

The Dfam database of repetitive DNA families

Robert Hubley  1 , Robert D Finn  2 , Jody Clements  3 , Sean R Eddy  4 , Thomas A Jones  4 , Weidong Bao  5 , Arian F A Smit  6 , Travis J Wheeler  7
Affiliations

The Dfam database of repetitive DNA families

Robert Hubley et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
Influence of average relative entropy on annotation for one family. This plot shows the impact of target average relative entropy values of the Charlie15a (DF0000089) model on both annotation coverage (true positives) and overextension. Using the Charlie15a seed, profile HMMs were built with HMMER's hmmbuild tool, with varying target average relative entropy values ranging from 0.4 to 0.9 bits per position, using the - -ere flag. The largest of these values represents the average relative entropy of the model when no sequence downweighting (entropy weighting) is performed. Coverage was assessed by searching each entropy-weighted profile HMM against the human genome. Overextension was assessed by searching each profile against a simulated genome containing fragments of true Charlie15a elements planted into realistic simulated genomic sequence built using GARLIC.
Figure 2.
Figure 2.
Impact of exponential entropy weighting on position-specific relative entropy. L1PREC2_5end (DF0000315) per-position relative entropy averaged over 30 bp windows with uniform and exponential entropy weighting functions. The region around position 1900 caused both false hits and overextension of true hits when using uniform entropy weighting; most of these were removed with the higher positional relative entropy generated using exponential entropy weighting.
Figure 3.
Figure 3.
Distribution of overextension lengths. Profile HMMs for human Dfam families were searched against an overextension benchmark trained on human sequence data, built using GARLIC. For each hit above GA threshold, overextension was calculated. The plot shows, for each overextension length, the number of hits with that length. Application of our two changes (increased average relative entropy and exponential entropy weighting) clearly reduced the frequency of very long overextensions.
Figure 4.
Figure 4.
Hit statistics for MLT1A (DF0001126).
Figure 5.
Figure 5.
Hits displayed on karyotypes. This plot shows the distribution of HAT1_CE (DF0001401) elements across C. elegans chromosomes, demonstrating the well-known accumulation of some DNA transposons towards telomeres (26,27).
Figure 6.
Figure 6.
Coverage, Conservation, and Insert plot for MIR (DF0000001).
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