Archive for the 'Releases' Category

Dfam 3.0 is out

March 6, 2019

 

The Dfam consortium is excited to announce the release of Dfam 3.0.  This release represents a major transition for Dfam from a proof-of-concept database into a funded open community resource. Central to this transition is a major infrastructure and technology update, enabling Dfam to handle the increasing pace of genome sequencing and TE library generation. Equally important, we merged Dfam_consensus with Dfam to produce a single resource for transposable element family modeling and annotation. In doing so, Dfam serves the needs of a broader research community while maintaining a high standard for family characterization (seed alignments), and TE annotation sensitivity. Finally, and most importantly, we are working on making Dfam a community driven resource through the development of online curation tools and direct user engagement.

Infrastructure updates

Dfam has undergone a major infrastructure upgrade since the last release including faster servers and storage systems, a new software stack and improved website features. Together these updates will allow Dfam to greatly expand the number of families and the species represented. The new software stack includes a publicly accessible REST API, which provides the core functionality used by the redesigned dfam.org website and is available for use in community developed applications and workflows. The new website is based on the Angular framework, supporting both a traditional web portal to the Dfam database as well as the use of interactive tools for data management and curation.

Dfam_consensus merger

The merger of Dfam_consensus with Dfam created a combined database of 6,235 TE families in 9 organisms, each characterized by a seed alignment of representative family members. Seed alignments constitute a rich dataset for generating sequence models such as consensus sequences, or profile Hidden Markov Models (HMMs).

Consensus sequence databases have traditionally not preserved the sequence alignment from which the consensus was generated. This omission has made it difficult to evaluate the strength of the consensus, to make incremental improvements by adding/removing members, or to regenerate models using improved methodologies. By adding support for consensus sequences to Dfam, the provenance is preserved in the seed alignment. In addition, the positions within the consensus can be directly related to the corresponding match states within the profile HMM.

Improved interfaces and metadata

The new Dfam website contains several features borrowed from Dfam_consensus including: the seed alignment visualization, the TE classification system and visualization, and per-family and full-database EMBL exports for consensus sequences.

TE classification tree visualization with search facility:

Figure1

In addition, we have improved the family browsing interface, and added the ability to store/visualize family features such as coding sequences, target site preferences, binding sites, as well as ad-hoc sequence annotation.

Coding regions and target site duplication details for Kolobok-1_DR:

Figure4

Dfam has adopted the recently developed (for Dfam_consensus) classification system for repetitive sequences and applied it to all of the Dfam-2.x families. This system combines concepts from established systems (Wicker et. al., Piegu et. al., Curcio et. al., Smit et. al., and Jurka et. al.) with phylogenies based on reverse transcriptase and transposases. Classification names were chosen to be as descriptive as possible while still honoring the most widely used acronyms for well-defined classes.

Dfam families may be queried using the new browse form:

Figure2

 

Community engagement

We are embarking on an effort to greatly expand the database using de-novo repeat identification pipelines, data sharing with other open-databases, and most importantly from direct community submissions. If you have existing TE libraries or plan to develop one for a newly sequenced organism, consider making it a part of the Dfam database. We can offer assistance with importing legacy datasets and are working on tools to facilitate direct community curation of the database. Please contact us at help@dfam.org.

Advertisements

Rfam 14.1 is out

January 28, 2019

We are happy to announce that a new Rfam release is now available! Rfam 14.1 includes 226 new families bringing the total number of Rfam families to 3,016. In addition, the R-scape visualisations have been updated to display pseudoknots, both manually annotated in seed alignments and predicted by R-scape (see below for details).

New families

The majority of the new families were contributed by Dr Zasha Weinberg (University of Leipzig) and were discovered by a systematic computational analysis of intergenic regions in Bacteria and metagenomic samples (see the NAR paper for more details). Many of the families come from environmental samples, so importing them into Rfam required a new procedure (described below).

This release features many families with statistically significant covariation (highlighted in green in the images below), for example Skipping-rope, Drum, and LOOT:

as well as a new unusually large, highly-structured RNA called ROOL that is found in Firmicutes, Fusobacteria and Tenericutes phylae as well as in phages and cow rumen metagenomic samples:

Browse new families in Rfam

Analysing pseudoknots using R-scape

Developed by Dr Elena Rivas (Harvard University), R-scape is a program that detects covariation support for structural pairs in RNA alignments (see the 2017 paper by Rivas et al in  Nature Methods for more details). Starting with version 1.2.0, R-scape systematically identifies pseudoknots supported by covariation (Rivas & Eddy, in preparation). For example, here is a pseudoknot from the SAM riboswitch that is not yet annotated in the Rfam seed alignment (left) but is correctly predicted by R-scape (right):

The nucleotides forming the pseudoknot are labelled pk_1, pk_2, pk_3 and so on in the structural annotation. Each pseudoknot is shown as a separate stem in an inset, and the basepairs with significant covariation are colored green similar to the other R-scape diagrams.

We are working on adding more pseudoknot annotations to the existing families based on the evidence from R-scape, 3D structures, and scientific literature. Please let us know if your favourite RNA is missing a pseudoknot.

Using RNAcentral identifiers in Rfam seed alignments

In previous releases, every sequence in every Rfam seed alignment was required to have an INSDC identifier assigned by a sequence archive like ENA or GenBank. However, when Rfam users submit their alignments to Rfam, they often include sequences that are not yet found in ENA or GenBank, especially if the sequences come from environmental samples. For example, sequence LV_Brine_h2_0102_1073789 from the MDR-NUDIX RNA does not exist in ENA so it does not have a stable identifier and is not associated with metadata such as NCBI taxid, description, or scientific literature.

In the past Rfam replaced such sequences with closely related ones or removed them altogether which required modifying the user-submitted alignments and could result in smaller, less informative seeds missing some covariation compared to the originals. In this release we implemented a new procedure that accepts RNAcentral identifiers in Rfam seed alignments in order to preserve the manually curated alignments as much as possible.

We began by importing the sequences and metadata from a recently established ZWD database (Zasha Weinberg Database) into RNAcentral where each distinct sequence is assigned a stable identifier (URS id) and linked to a NCBI taxid, its parent ZWD alignment, and scientific literature. For example, sequence LV_Brine_h2_0102_1073789 is assigned RNAcentral id URS0000D661D6_12908 so that it can be easily tracked using RNAcentral search, API, public database, or bulk download files.

Next we replaced the ZWD identifiers with RNAcentral accessions and used the ZWD-RNAcentral alignments as seeds for new Rfam families:

Following the standard Rfam protocol, we manually selected bit-score thresholds for each family that allow reliable identification of sequences from the seed alignments and other homologs from the Rfam sequence database.

A small number of sequences still had to be removed from ZWD alignments in the following cases:

  1. If a covariance model built using the alignment could not find some of its own sequences, these unmatched sequences were removed from the alignment
  2. If a sequence scored worse than a set of random sequences that serve as control when setting bit-score thresholds, such low-scoring sequences were also removed from the alignments.


In future releases we plan to expand the usage of RNAcentral identifiers in Rfam seed alignments.

Please note that any software that parses Rfam seed alignments and uses ENA or GenBank for metadata lookup will now need to include RNAcentral identifiers using the RNAcentral API. For more information or if you have any questions, please contact the RNAcentral team or Rfam help.

11 more families with 3D structure

There are 11 additional Rfam families that match 3D structures bringing the total number of families with experimentally determined structures to 98 (compared with 87 in Rfam 14.0).

Rfam familyPDB structures
RF00009 (RNaseP_nuc)6agb and 6ah3 (yeast), 6ahr and 6ahu (human) [chains A]
RF00025 (Telomerase-cil)6d6v (chain B)
RF00027 (let-7)5zal (chain C), 5zam (chain C)
RF00080 (yybP-ykoY)6cc1 (chains A and B), 6cc3 (chains A and B)
RF00233 (Tymo_tRNA-like)6mj0 (chains A and B)
RF00250 (mir-TAR)6gml (chain P)
RF00390 (UPSK)6mj0 (chains A and B)
RF01727 (SAM-SAH)6hag (chain A)
RF01826 (SAM_V)6fz0 (chain A)
RF02348 (tracrRNA)6mcb (chain B), 6mcc (chain B)
RF02553 (YrlA)6cu1 (chain A)

Other updates

Two existing families were updated with new seed alignments from ZWD, including RF02440 (ldcC RNA) and RF02840 (Lacto-3 RNA). There is also a new clan DUF805 (CL00115) that includes DUF805 and DUF805b families.

Acknowledgements

The Rfam team would like to thank Dr Elena Rivas and Dr Zasha Weinberg for the new data, software, and feedback, as well as the organisers and participants of the 2018 Benasque RNA meeting. We would also like to thank BBSRC for funding Rfam between 2015 and 2018.

Get in touch

Follow Rfam on Twitter to find out about new Rfam families and don’t hesitate to raise a GitHub issue or email us if you have any questions.

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.

Introducing Dfam_consensus – Dfam’s consensus sequence twin

May 18, 2017

Since its inception in 2012, Dfam has demonstrated the promise of using profile hidden Markov Models (HMMs) to improve the detection sensitivity and annotation quality of Transposable Element (TEs) families in human[1] and subsequently for four additional reference organisms[2].  Despite these advances, the tools used to discover new families ( de-novo repeat finders ), improve families ( extend, defragment, subfamily clustering ), and classify TE families continue to depend on consensus sequence models.  This discordance between methodologies is a direct impediment to Dfam’s expansion.

Read the rest of this entry »

Pfam 31.0 is released

March 8, 2017

Pfam 31.0 contains a total of 16712 families and 604 clans. Since the last release, we have built 415 new families, killed 9 families and created 11 new clans.  We have also been working on expanding our clan classification; in Pfam 31.0, over 36% of Pfam entries are placed within a clan. Read the rest of this entry »

Pfam 30.0 is available

July 1, 2016

Pfam 30.0, our second release based on UniProt reference proteomes, is now available. The new release contains a total of 16,306 families, with 22 new families and 11 families killed since the last release. The UniProt reference proteome set has expanded and now includes 17.7 million sequences, compared with 11.9 million when we made Pfam 29.0. In this release, we have updated the annotations on hundreds of Pfam entries, and renamed some of our Domains of Unknown Function (DUF) families.

DUFs are protein domains whose function is uncharacterised. Over time, as scientific knowledge increases and new data about proteins comes to light, more information about the function of a domain may become available. As a result, DUFs can be renamed and re-annotated with more meaningful descriptions. As part of Pfam 30.0, we have re-annotated 116 DUFs based on updated information in the UniProtKB database, the scientific literature, and feedback from Pfam and InterPro users. Examples of some our DUF updates in Pfam 30.0 are given below:

 

  • PF10265, created in release 23.0 and originally named DUF2217, has been renamed to Miga, a family of proteins that promote mitochondrial fusion.
  • PF10229, created in release 23.0 and originally named DUF2246, has been renamed as MMADHC, as it represents methylmalonic aciduria and homocystinuria type D proteins and their homologues.  The structure of this domain is shown below.

 

5cv0

Structure of MMADHC dimer, PDB:5CV0

 

  • PF12822, created in release 25.0 and originally named DUF3816, has been renamed to ECF_trnsprt, since it contains proteins identified as the substrate-specific component of energy-coupling factor (ECF) transporters.

Please note that we may change the identifier for a family (e.g. DUF2217), but we never change the accession for a family (e.g. PF10265).

If you find any more DUFs that can be assigned a name based on function, or any other annotation updates, please get in touch with us (pfam-help@ebi.ac.uk).

 

Pfam 29.0 is now available

December 22, 2015

Pfam 29.0, our second release of 2015, contains 16295 entries and 559 clans. We have made some major changes to our underlying sequence database and the data that are displayed on the website, which we’ve outlined below. Full details can be found in our Nucleic Acids Research paper, which is available here. Read the rest of this entry »

Meet Dfam2.0

October 30, 2015

Dfam is growing up. This is the first major expansion of the database since it’s inception. We’ve added repeat families from four new organisms: mouse, zebrafish, fruit fly, and nematode. In total, this release includes 2,844 new familes ( 4,150 total ).

Read the rest of this entry »

Say hello to Dfam1.4

May 13, 2015

With Dfam, we are striving to build models of repeat families that yield high sensitivity without undue false annotation.  In this release of Dfam, we have improved our model building strategy to reduce the potential for false annotation, especially in the context of overextending alignments around true interspersed repeat instances.

Read the rest of this entry »