Posts Tagged ‘dfam’

Curation with Dfam: new data and platform updates

March 17, 2020

DNA transposon termini signatures

The Dfam consortium is excited to announce the generation and release of terminal repeat sequence signatures for class II DNA transposable elements. The termini of class II elements are crucial for movement, and as such, can be used to classify de novo DNA transposable element families in new genomic sequences (Figure 1).

Figure 1. Major subgroups of class II DNA transposons.

The LOGOs of the termini can be viewed on the “Classifications” tab on the Dfam website and are organized by class II subclasses (e.g., Crypton, Helitron, TIR, etc.) (Figure 2). This allows for easy visualization of the base conservation at each position in the terminal sequences and comparisons between the 5’ and 3’ termini (Figure 2). In addition, the termini profiles are available for download as a .HMM file.

Figure 2. Termini signature visualization on the Dfam website (www.dfam.org) sample. Base conservation can be seen via the LOGOs of the 5’, 3’ and combined edge (termini) HMMs. The movement type can be seen preceding DNA transposons that move via a common mechanism (e.g. “Circular dsDNA intermediate). The number of families used to generate the LOGOs are indicated, as well as the subclass named (e.g. “Crypton_A”). Additional notes on the termini, when relevant, are also available.

Community data submissions

We have taken the first small step towards a community-driven data curation platform by developing a new data submission system.  At the start this will facilitate the process of uploading data to the site for processing by the curators. As we move forward, further aspects of the curation process will be made available to the community.  Upon creating an account and logging in, users can submit files to Dfam using our web-based upload page. Here you will also find information about submission requirements and how different levels of library quality are handled in Dfam.

Moving to xfam.org

May 1, 2014

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 »

TreeFam 9 is now available!

May 3, 2013

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
  • new tree visualisations in pure javascript using D3, e.g. see the BRCA2 gene tree here.
  • 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.

Happy treefamming,

the TreeFam team
(Fabian, Mateus)

Dfam paper is an NAR “featured article”; RepeatMasker4 is out

January 12, 2013

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

Dfam 1.1 released

November 15, 2012

We are pleased to announce that we’ve released Dfam 1.1. This version represents a few important changes from 1.0, including updated hit results, a new tab for each entry page showing relationships to other entries, and improved handling of redundant profile hits.

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Dfam: A database of repetitive DNA elements

September 6, 2012

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.

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