Back in November 2012 we announced that the Xfam team in the UK was moving from the Wellcome Trust Sanger Institute to the European Bioinformatics Institute (EMBL-EBI), just next door on the Wellcome Trust Genome Campus. On Tuesday we completed that move by switching off the Pfam and Rfam websites inside Sanger and redirecting all traffic to our shiny new home at xfam.org. You can now find the Pfam and Rfam websites at pfam.xfam.org and rfam.xfam.org respectively. Read the rest of this entry »
Posts Tagged ‘dfam’
We are happy to announce that TreeFam 9 is online and you can find it under http://www.treefam.org.
TreeFam 9 now has 109 species (vs. 79 in TreeFam 8) and is based on data from Ensembl v69, Ensembl Genomes v16, Wormbase and JGI.
This release marks an important step for TreeFam as it is the first release build since TreeFam has been resurrected.
Here is a list of the most important changes in TreeFam 9:
- New website layout (adopting the Pfam/Rfam/Dfam layout)
- Infrastructure move of web servers and databases to the EBI
- Sequence search against the library of TreeFam family profiles
- Pairwise homology download
We hope you find all the information you are looking for. If you don’t, please let us know so that we can include the information you want. The old website will remain online here.
If you have questions, suggestions or find bugs, don’t hesitate to contact us through our new forum here.
the TreeFam team
We are pleased to announce that the Dfam paper (“Dfam: a database of repetitive DNA based on profile hidden Markov models“) is now available in the 2013 NAR Database issue, and has been selected as a “featured article” (meaning the NAR editorial board thinks it is among “the top 5% of papers in terms of originality, significance and scientific excellence”).
In other exciting news, two members of the Dfam consortium, Arian Smit and Robert Hubley (Institute for Systems Biology, Seattle), just released RepeatMasker 4.0. This is a major update that, among other important improvements, adds support for searching with Dfam and nhmmer. Go get yourself a copy at http://www.repeatmasker.org/
Posted by Travis
We are pleased to introduce Dfam 1.0, a database of profile HMMs for repetitive DNA elements. Repetitive DNA, especially the remnants of transposable elements, makes up a large fraction of many genomes, especially eukaryotic. Accurate annotation of these TEs both simplifies downstream genomic analysis and enables research into their fascinating biology and impact on the genome.