Posts Tagged ‘rfam’

Rfam 14.0 is out with over 100 new families and an expanded genome collection

August 8, 2018

Rfam14_coverHQ

We are happy to announce that the new release of Rfam, version 14.0, is now available! Rfam 14.0 is built using a set of over 14,000 non-redundant, representative, and complete genomes (~60% more than in Rfam 13.0). It includes 105 new families, new genome browser hub, and ORCiD integration. Read on to find out more.

What’s new

Data updates

Rfam 14.0 has 60% more genomes than Rfam 13.0

The latest Rfam version comes on the heels of Rfam 13.0, a release that marked the transition to the genome-centric sequence database. In Rfam 13.0, the Rfam sequence database – Rfamseq – was composed of 8,364 non-redundant, representative and complete genomes derived from a genome collection maintained by UniProt. Now with the addition of 6,519 new species, the number of annotated genomes in Rfam 14.0 increased by ~60% to 14,434 genomes.

Screen Shot 2018-08-08 at 3.17.20 PM

The majority of the genomes from Rfam 13.0 are also present in Rfam 14.0, although a small number (385, ~4.6%) was removed or replaced. The majority of the new genomes come from Bacteria and Viruses.

Since Rfamseq was updated, this is a major Rfam release (14.0). Expect a minor release (14.1) in the Fall 2018 with new RNA families but no changes in Rfamseq.

More genomes, less redundancy

The switch to annotating complete genomes enabled us to resolve data redundancy at the levels of sequence and species. For instance, in Rfam 12.3 the cumulative length of all human sequences was eight times longer than the total length of the human genome assembly hg38 in 13.0 (note how the width of the green line of Rfam 12 narrows in Rfam 13).

Screen Shot 2018-08-08 at 3.17.45 PM

Redundancy reduction at species level relies on Uniprot’s reference proteome collection, which is a result of manual curation and computational refinement. It includes species of high interest to the scientific community and well-studied model organisms, carefully selected in such a way that they represent the taxonomic diversity. Rfam uses the same collection of genomes for annotation with existing RNA families and building new ones.

105 new families

The number of RNA families reached 2,791 with the addition of 105 new families from 8 RNA types. The new families per ncRNA type in release 14.0 is shown below:

  • 65   Gene; sRNA;
  • 17   Gene; antisense;
  • 11   Gene; snRNA; snoRNA; HACA-box;
  • 5     Gene; snRNA; snoRNA; CD-box;
  • 4     Cis-reg; thermoregulator;
  • 1     Cis-reg;
  • 1     Cis-reg; leader;
  • 1     Cis-reg; riboswitch;

Browse 105 new families

New 3D structures matching Rfam families

2 more Rfam families now have experimentally determined 3D structures that did not match any 3D structures in the past:

Rfam family PDB structure
RF00382 DnaX ribosomal frameshifting element 5UQ7, 5UQ8 – 70S ribosome complex with dnaX mRNA stemloop and E-site tRNA (“in” and “out” conformation)
RF00375 HIV primer binding site 6B19 – Architecture of HIV-1 reverse transcriptase initiation complex core

Search for Rfam entries in PDBe

Rfam regularly updates the mapping between Rfam families and the experimentally determined 3D structures available in PDB. With PDBe’s Advanced Search release in May 2018, PDBe users can take advantage of these mapping by searching with Rfam family names or accessions. For instance, a search using tRNA accession RF00005 currently retrieves 502 entries.

Another powerful new feature is the interactive 3D visualization of the Rfam domains on PDBe entry pages using LiteMol. This is achieved by highlighting the RNA sequence on the corresponding structure, for example tRNA (RF00005) in structure 4UJD. Additional information can be found in the PDBe blog post.

Increased GO term coverage

Non-coding RNA functional annotation was improved with the addition of 133 GO terms to 81 families since last release. The GO annotations are propagated to RNAcentral sequences and submitted to the GOA system, as described in GOREF:0000115.

Genome browser hub

The genome-centric sequence database enabled us to generate the genome browser track hub directly out of the genome annotations without an additional mapping step. At this time we limited the species listed in track hub to those supported by UCSC, with the potential of that number to grow by incorporating all genomes with assemblies at chromosome level. Currently there are 14 species including human (hg38), chicken (galGal5), pig (susScr11) and mouse (mm10). Upon user request, we will also be happy to provide .bed and .bigBed files for various other genomes in our collection, depending on the level of the assembly.

Explore Rfam annotations in UCSC Genome Browser by clicking on these links:

or configure the track manually by editing the URL:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr1&hgct_customText=track%20type=bigBed%20name=Rfam%20description=%22Rfam%2014.0%20ncRNA%20annotations%22%20visibility=full%20bigDataUrl=ftp://ftp.ebi.ac.uk/pub/databases/Rfam/14.0/genome_browser_hub/homo_sapiens/bigBed

The track hub can also be attached to Ensembl using these instructions and the following URL:

ftp://ftp.ebi.ac.uk/pub/databases/Rfam/14.0/genome_browser_hub/hub.txt

Get credit for Rfam families using ORCiD

It is now possible for Rfam authors to get credit for their contributions by claiming family accessions directly to their ORCiD profiles. This new feature was enabled by the Claim to Orcid functionality provided by EBI Search. The process includes three simple steps. Users are first required to login to their ORCiD accounts and use their ORCiD id to search for associated entries. Following search, one can manually select all or a subset of listed entries and click on Claim to ORCID button located at the top of the page. The example provided is of a snoRNA family (RF02725) claimed by the Rfam curator Joanna Argasinska directly to her ORCiD profile.   

New Rfam paper

rfam-cpb-paperWe recently published a new paper in Current Protocols in Bioinformatics with examples covering a broad spectrum of Rfam use cases including examples using our website as well as Infernal to annotate nucleotide sequences. There is also a section dedicated to MySQL with tips and tricks on restoring previous versions of the database, along with useful examples on forming complex queries.

Get in touch

Follow our new Twitter account RfamDB to be the first to find out about new Rfam families and don’t hesitate to raise a GitHub issue or email us if you have any questions.

You can also meet the Rfam team in person at a hands-on tutorial at the upcoming ECCB 2018 conference in Athens.

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Genome-centric Rfam is finally here!

September 15, 2017

rfam-13.0We are pleased to announce the release of Rfam 13.0, the first major update since Rfam 12.0 went live in 2014. In this version we introduce a new genome-centric sequence database composed of non-redundant, representative, and complete genomes, as well as new website features, such as an updated text search.

Find out more about Rfam 13.0 in the NAR paper by Kalvari et al.: Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.

Rfam 12.3 is out

June 29, 2017

rfam_12_3_cover_720

The new Rfam release (version 12.3) features 101 new families, unified search, and updated documentation.

New families

Rfam 12.3 featured families

In this release 101 new families were added to the database, including over a dozen Yersinia pseudotuberculosis RNA thermometers from a recent PNAS paper by Righetti et al. We would like to thank Zasha Weinberg for contributing NiCo riboswitch, Type-P5 Twister, and several RAGATH RNAs (for example, RAGATH-5). You can browse the new families here.

Unified text search

Rfam text search

Over the years Rfam developed many specialised ways of searching and exploring the data, such as Keyword search, Taxonomy search, browsing entries by type, and “Jump To” navigation. While these options work well, they may be confusing for new users, so we set out to unify all search functionality in a single text search.

The new search is available on the Rfam homepage or at the top of any Rfam page and is powered by EBI search. It allows to browse RNA families, clans, motifs, or explore Rfam by category using facets. For example, one can view families with 3D structures or view all snoRNA families that match human sequences, and the URLs can be bookmarked or shared.

The new search is a full replacement for the old search functionality except for taxonomy, because the new search can find species but not higher-level taxa. For example, one can search for Homo sapiens but not for Mammals. Stay tuned for future updates and use the old Taxonomy search in the meantime. We plan to retire all old search functionality once the new search is fully developed but until then the old and the new searches will coexist.

For more information about the new search, see Rfam documentation. If you have any feedback, please let us know in the comments below, on GitHub, by email, or on Twitter.

New home for Rfam documentation

Rfam help has been migrated to a dedicated documentation hosting platform ReadTheDocs and is now available at http://rfam.readthedocs.org.

Rfam ReadTheDocs help

The new system offers several advantages:

The source code of the documentation is available on GitHub so if you notice a problem you can let us know by creating an issue or help us fix it by editing the text on GitHub and sending a pull request.

Other updates

  • Clan competition for PDB entries: Now the 3D structure tab, the public MySQL database, and the FTP archive show only the lowest E-value match when several RNA families from the same clan match a PDB chain. For example, chain 0 of PDB structure 1S72 (LSU rRNA from an Archaeon Haloarcula marismortui) now matches only the Archaeal LSU family instead of all families from rRNA LSU clan.
  • New 5S rRNA clan CL00113 that includes 5S rRNA and mtPerm-5S families.

What’s next

This release will be the last “point release” for Rfam 12. In the next few months we will release Rfam 13.0 which will be based on a new sequence database. Previously, Rfam annotated WGS and STD subsets of ENA, which grow very quickly and include many redundant sequences. We will take advantage of reference genomes from UniProt reference proteome collection which is a regularly updated, reduced-redundancy set of reference genomes. This allows us to perform meaningful taxonomic comparisons and explore RNA families by taxonomy without sifting through thousands of versions of the same genome.

Get in touch

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

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)