Dfam: annotation of transposable elements with profile HMMs

We’re happy to announce the release of Dfam 1.0, a set of profile HMMs for genomic DNA annotation of transposable elements. This essentially constitutes an upgrade of repeat element annotation from using searches with single sequence consensuses to using searches with profile HMMs, now that the HMMER3 project has made DNA/DNA profile HMM searches sufficiently fast for whole genomes. Dfam is a collaboration between Jerzy Jurka and his Repbase resources (Genetic Information Research Institute), Arian Smit and his RepeatMasker software (Institute for Systems Biology, Seattle), the HMMER3 development team at Janelia Farm (particularly Travis Wheeler, leading nhmmer development), and the Xfam database consortium (particularly Rob Finn, here at Janelia). Among other effects of this work, we expect the widely used RepeatMasker software to include nhmmer, Dfam models, and profile HMM searches in the near future. A preprint of the first Dfam paper is available now on our preprint server, and the database itself is available for use at dfam.janelia.org.
Continue reading