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

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.

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).

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:

• Human (hg38)
• Mouse (mm10)
• Chicken (galGal5)
• Pig (susScr11)

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

We 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!

We 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

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

New 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

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.

The new system offers several advantages:

• the documentation is searchable using a built-in search engine
• the content can be easily updated using GitHub collaboration tools without any web development skills. Anyone can contribute on GitHub, and we would like to thank Natalia Quinones-Olvera and Eric Nawrocki for their help.

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.

Join Rfam, see the world

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?

The Rfam 10.1 release is out!

The crowd of people behind Rfam are proud to announce a new release of the Rfam database. This is version 10.1 and is mostly an increase in the number, size and quality of families.

Rfam now has 1973 families, 528 more families than the 10.0 release. We are just one prokaryotic RNA-seq project away from hitting 2000 families! In fact, we have passed 2000 in terms of Rfam accession (RF02031 is the Escherichia coli sRNA, tpke11). My selfish attempt to claim the coveted RF02000 accession was snatched from my grasp by Chris Boursnell who added RF02000 which now corresponds to the rice microRNA MIR1846 from the miRBase database. I did claim RF01999 and RF02001 with two
sub-types of Group II catalytic intron domains 1-4 that Zasha Weinberg kindly provided to Rfam.

The new families included nearly 100 novel elements inferred by Zasha Weinberg and colleagues in his recent Genome Research article [1]. Zasha kindly provides Rfam with the alignments and writes Wikipedia articles for each notable element, greatly easing the burden on Rfam for incorporating these into the database.

Our new recruit, Ruth Eberhardt, originally from the UniProt group at EBI, has also made a significant mark on the new release. Ruth has been busily incorporating “domains” derived from long messenger-like non-coding RNAs (a.k.a. lncRNAs). These are regions within each transcript that are unusually well conserved and there is some evidence that secondary structure within the regions is evolutionarily constrained. The new families include: MEG3, MALAT1, MIAT, PRINS, Xist, TUG1, HSR-omega, Evf1, HOTAIR, KCNQ1OT1, SOX2OT, NEAT1, EGOT, H19 and HOTAIRM1.

This summer we had the pleasure of hosting another talented summer student, Ben Moore. Ben is a prolific Wikipedian and rapidly made his mark on the RNA Wikipedia entries and continues to do so while working on a MRes in Computational Biology at the University of York. One stunning feat Ben accomplished was passing the article for “Toxin-antitoxin system” through Wikipedia’s peer-review process for “good articles”. This process appears to be at least as rigorous as scientific peer-review and is quite an achievement. He also built a number of families for RNA anti-toxins including Sok, RNAII, IstR, RdlD, FlmB, Sib, RatA, SymR and PtaRNA1. PtaRNA1 is a newly discovered RNA antitoxin that was first published by Sven Findeiss and colleagues in the RNA families track at RNA Biology. This track has provided very useful updates and expansions for Rfam directly from the RNA community.

A guest Rfam rogue, Chris Boursnell, who has been visiting from Andrew Firth’s group has also been busy building new families. With permission from the good people at the Recode-2 database [3] Chris has added a number of new frame-shift elements and has also updated a number of microRNA families based on the latest release of miRBase [4].

An enormous achievement for the database is the inclusion of full-length small subunit ribosomal RNA families. Previously Rfam had just one truncated model that covered all three kingdoms of life. Thanks to the hard work of Eric Nawrocki and colleagues in Sean Eddy’s lab on the Infernal software and related package ssu-align which can now deal with much larger datasets than were previously possible. The three new alignments now cover bacteria, archaea and eukaryotes. These are all derived from the highly accurate and excellent alignments from the work of Robin Gutell and colleagues who run the Comparative RNA Website.

Thanks to the exciting work by Stefan Washietl and colleagues on the RNAcode software package we now have good evidence that the “RNA” family, C0343 (RF00120), is in fact protein-coding and most-likely is not functioning as a RNA other than in a mRNA-sense [5]. Therefore C0343 has been removed for the 10.1 release.

Our SRP families have all been rebuilt and supplemented with additional families thanks to the work of Magnus Rosenblad and colleagues [6]. This is another excellent contribution to the RNA families track at RNA Biology. Based on this work the existing two SRP families were replaced and supplemented by 7 new families: Metazoa_SRP (RF00017), Bacteria_small_SRP (RF00169), Fungi_SRP (RF01502), Bacteria_large_SRP (RF01854), Plant_SRP (RF01855), Protozoa_SRP (RF01856) and Archaea_SRP (RF01857). These new models should improve the specificity of Rfam annotations and reduce the number of pseudogenes incorporated.

We have continued to work on the Rfam clans and have added 3 new clans. These are U3 (CL00100), Cobalamin (CL00101) and group-II-D1D4 (CL00102). Also, the membership of the clans tRNA (CL00001), RNaseP (CL00002) and SNORA62 (CL00040) have been updated.

Finally, several problematic microRNA families mir-544 (RF01045), mir-1302 (RF00951), mir-1255 (RF00994), mir-548 (RF01061), mir-649 (RF01029), mir-562 (RF00998) and spliceosomal U13 (RF01210) were rethresholded to remove the excessive number of pseudogene annotations in the full alignments. This rethresholding along with the rebuilding of our SSU models have removed approximately 600,000 annotations from Rfam.

There are countless other changes that have made, if I’ve forgotten to include any that are significant to you or to mention your name then I apologise profusely.

This release could not have happened without the invaluable help of Jen Daub and John Tate who have worked tirelessly and enthusiastically on this release. This was made particularly challenging by the fact that I have recently relocated to my homeland in New Zealand to take up a position as a Rutherford discovery fellow and senior lecturer at the University of Canterbury in Christchurch. I hope to continue to contribute to Rfam and the wider RNA community from here. This is also a good moment to welcome the new Czars of Rfam, Sarah Burge and Eric Nawrocki who will now face the exciting and challenging task of managing the day-to-day work of maintaining Rfam. I wish them the best of luck in their new roles. I hope they enjoy it as much as I have.

Paul Gardner.

References

[1] Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR. (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biology. 11(3):R31.

[2] Findeiss S, Schmidtke C, Stadler PF, Bonas U (2010). A novel family of plasmid-transferred anti-sense ncRNAs. RNA Biology. 7 (2): 120–4.

[3] Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV. (2010) Recode-2: new design, new search tools, and many more genes. Nucleic Acids Res. 38(Database issue):D69-74.

[4] Kozomara A, Griffiths-Jones S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research. Jan;39(Database issue):D152-7.

[5] Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. (2011) RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA. 17(4):578-94.

[6] Rosenblad MA, Larsen N, Samuelsson T, Zwieb C. (2009) Kinship in the SRP RNA family. RNA Biology. 2009 Nov-Dec;6(5):508-16.