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.
The team behind Rfam is pleased to announce the release of Rfam 11.0. This release represents a major update from 10.1, primarily due to the upgrade of our underlying sequence database, Rfamseq.
We’ve had a few helpdesk tickets in the last few months asking how to download all of the Pfam-A domains for a particular species. This information can be quite difficult to obtain: getting it requires either downloading and installing a sub-set of the tables in our MySQL database, or else searching all of the sequences from the species of interest against Pfam, probably using our batch search.
Two related questions that we are often asked via the Pfam helpdesk is ‘Which families have a known three-dimensional structure?’ and ‘Why is a particular a PDB structure not found in Pfam’. You may think that there are obvious answers to these questions – but as with many things in life the answer is not necessarily as straight forward as you would have thought. In this joint posting between Andreas Prlic (senior scientist at RCSB Protein Data Bank) and myself (Rob Finn, Pfam Production Lead), we will elaborate on the way the PDB and Pfam cross referencing occurs, why discrepancies occurred in the past and describe the pipeline that the RCSB PDB has implemented using the HMMER web services API, which should provide the most current answer to these questions. Read the rest of this entry »