Dfam is growing up. This is the first major expansion of the database since it’s inception. We’ve added repeat families from four new organisms: mouse, zebrafish, fruit fly, and nematode. In total, this release includes 2,844 new familes ( 4,150 total ).
Archive for the 'Releases' Category
With Dfam, we are striving to build models of repeat families that yield high sensitivity without undue false annotation. In this release of Dfam, we have improved our model building strategy to reduce the potential for false annotation, especially in the context of overextending alignments around true interspersed repeat instances.
We are pleased to announce the release of Dfam 1.3. This release includes almost 200 new repeat families and updates the underlying human genome to hg38.
We are pleased to announce that we’ve released Dfam 1.2. This version represents a few important changes from 1.1, including increased sensitivity for many families, a new plot on the model page, and an improved Relationships tab.
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
In a blog post published just over a year ago, I proposed a number of changes to the content of Pfam to improve scalability and usability of the database. These changes came into effect a few days ago, when we released Pfam 27.0. This release of Pfam contains a total of 14831 families, with 1182 new families and 22 families killed since release 26.0. 80% of all proteins in UniProt contain a match to at least one Pfam domain, and 58% of all residues in the sequence database fall within a Pfam domain. Read the rest of this entry »
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 have recently produced a new release of AntiFam, release 3.0. AntiFam has grown in size, and release 3.0 contains 54 entries – compared to just 23 when we last blogged about AntiFam (release 1.1). Over 80 % of these new entries arise from translations of non-coding RNAs, including several families from translations of rRNA, tmRNA and RNaseP.
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.