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
Behind the scenes we are working hard on building the next TreeFam release, which will be TreeFam 9.
TreeFam 9 will have 109 species, that is a 37% increase over TreeFam 8. Most of the species come from EnsEMBL (v.69) and EnsEMBL genomes (v.16) with a few ones coming from JGI.
Besides that – and probably most important for the user – will be our new web site. Based on the success of other Xfam-databases like Pfam , Rfam  and -most recently- Dfam , we decided to give the TreeFam website a face lift by adapting it to the Xfam look&feel.
So, there are great things to come and soon we will have our next blog post.
The next TreeFam blog post will then be about TreeFam 9!
For some light weekend reading, have a look at the latest Rfam paper, Rfam 11.0: 10 years of RNA Families. It’s part of the 2013 Nucleic Acids Research Database issue, and you’ll find all the latest developments to Rfam mentioned, including the sunbursts, the Biomart and an update on the Wikipedia annotation effort.
We are pleased to announce the inclusion of R-chie arc diagrams in the Rfam family secondary structure galleries. We think these images are beatiful and intuitive ways of visualising complex RNA secondary structures, and we hope that you find them as useful as we do. You can find the R-chie tab in the secondary structure image gallery for each family; from there you can zoom in and out of the images, as well as viewing the image in a seperate window. The majority of Rfam families have R-chie images; those which don’t are families without secondary structure. Have a look at the U1 spliceosomal RNA, or tRNA for examples.
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.
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.
After 15 great years at the Sanger Institute we are on the move. On the 1st November, the Cambridge Xfam group will be taking up residence at the European Bioinformatics Institute on the other side of the Wellcome Trust Genome Campus. We’ll keep running the websites at Sanger for a bit longer, but eventually we’ll get them migrated over to EBI webspace. We’re hoping that the move will not cause any disruption to our users, but we might be a little bit slower at responding to your questions and bug reports.
We’ll keep you posted on updates to the website and database locations using the blog and our Twitter account.
We’ve now made it easier for Rfam users to submit an alignment of a new family, or an improvement to an existing family in Rfam. As long as you have a Stockholm format alignment, you can use our web form to submit your alignment. Read the rest of this entry »
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.