Posts Tagged ‘rfam’

Rfam 12.2 is live

January 25, 2017

We are happy to announce a new release of Rfam (version 12.2) which includes 115 new families, introduces R-scape secondary structure visualisations, and restores missing families to multiple Rfam clans.

New families

This release adds 115 new Rfam families bringing the total number of families to 2,588. Notable additions include Pistol, Hatchet, Twister-sister and several other riboswitches contributed by Zasha Weinberg. We are always looking for new RNA families, so please feel free to get in touch with your suggestions.

Testing covariation with R-scape

R-scape is a new method for testing whether covariation analysis supports the presence of a conserved RNA secondary structure. In order to check the quality of Rfam structures, we ran R-scape on all Rfam seed alignments and added R-scape visualisations to the secondary structure galleries. For example, here is R-scape analysis of the SAM riboswitch:

r-scape-sam-riboswitch

According to R-scape, the secondary structure from the Rfam seed alignment, shown on the left, has 19 statistically significant basepairs (highlighted in green). R-scape can also use statistically significant basepairs as constraints to predict a new secondary structure that is consistent with the seed alignment. Using this approach, R-scape increased the number of statistically significant basepairs from 19 to 27 while also adding 9 new basepairs that are consistent with the seed alignment (structure on the right). This visualisation gives an idea about the quality of the Rfam structure and indicates that in this case it may need to be updated. To find out more about R-scape have a look at a recent paper by Rivas et al.

Tip: R-scape visualisations are interactive, so you can pan and zoom the structures and get additional information by hovering over nucleotides and basepairs.

R-scape analysis suggests that many existing Rfam secondary structures can be improved (for example, FMN riboswitch or 5S rRNA). In other families secondary structures are not supported by the R-scape covariation analysis (for example, oxyS RNA) which indicates that either their seed alignments need to be expanded or that these RNA families do not have a conserved secondary structure. Lastly, there are also cases where the R-scape structures do not show significant improvement compared to the current secondary structure (for instance, Metazoa SRP).

In future releases we will begin to improve existing Rfam seed alignments by using R-scape in the family building pipeline. In the meantime, Rfam users can get an indication of the quality of the structure using R-scape visualisations.

Recovering lost clan members

Since Rfam 10.0, related Rfam families have been organised into clans. The clans are manually curated and clan membership is checked using automated quality control steps (for example, to make sure that a family cannot belong to more than one clan). However, under certain circumstances these quality control procedures silently removed families from the clans. This bug was introduced in Rfam 11.0, and over time, more than 30 families were dropped from 20 clans, so that some clans did not have any families at all. The problem has now been fixed and proper clan membership has been restored using Rfam releases from the FTP archive. You can explore Rfam clans and let us know if you have any feedback.

Other updates

How to access the data

In addition to the Rfam website, you can access the data in the FTP archive and via the API. There is also a public MySQL database introduced in the last release.

What’s next

As well as revisiting Rfam seed alignments, work is underway on the next major Rfam release (13.0) which will be based on a new sequence database built from complete genomes. We plan to make the new data available in late 2017.

Get in touch

We always welcome comments and feedback about Rfam, so feel free to get in touch by email or by submitting a new GitHub issue.

Rfam 12.1 has been released

April 27, 2016

Rfam 12.1 announcement

We are happy to announce a new release of Rfam. Version 12.1, based on the same sequence dataset as Rfam 12.0, features over 20 new families, a new clan competing algorithm, a publicly accessible MySQL database, and many website fixes.

Read the rest of this entry »

Rfam 12.0 is out

September 24, 2014

We are pleased to announce the release of Rfam 12.0! Read the rest of this entry »

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 »

Join Rfam, see the world

January 31, 2014

Rfam is recruiting! We are currently recruiting an RNA informatician to join our team. We’re looking for someone really enthusiastic about RNA and who’s interested in working with Rfam as we move to genome-based alignments and explore new technologies for the database and website.

If this is you, why not apply to join us as a Senior Bioinformatician?

We’ve moved, now the websites

January 30, 2014

In November 2012, we announced that the Xfam groups were moving the few tens of metres from the Wellcome Trust Sanger Institute to the European Bioinformatics Institute. We warned you then, that the websites would also eventually move. 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)

The Rfam NAR paper is now available!

November 23, 2012

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.

R-chie arc diagrams now available in our secondary structure galleries

November 19, 2012

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.

The R-chie diagrams are created using the R4RNA R package from Irmtraud Meyer’s group; be sure to check out the R-chie paper, as well as their own gallery of Rfam structures.

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.

Read the rest of this entry »