Secondary structure diagrams for LSU rRNA
We continue to expand the coverage of the RNA secondary structure space. After generating diagrams for SSU and 5S rRNA as well as >2,000 Rfam families, we now provide secondary structure visualisations for the large ribosomal subunits (LSU). For example, here are the human and the Escherichia coli LSUs displayed using single-page layouts:
This work was done in collaboration with Anton S. Petrov and Loren Dean Williams from the Center for the Origins of Life (COOL) at Georgia Tech, who generated 17 manually curated LSU templates based on the experimentally determined 3D structures. These templates cover a wide taxonomic distribution in order to accurately model the expansion segments. The auto-traveler software now supports the LSU templates and generated >100,000 LSU diagrams.
For the first time it is possible to visualise some of the largest known structured RNAs using a fully automatic approach. Explore the new structures and read on.
40 Expert Databases and counting
With this release RNAcentral reaches a milestone of 40 member databases! We have added 5 new resources that provide in-depth information about 5S rRNA, microRNAs, snoRNAs, a wide range of human non-coding RNAs, as well as human disease-associated non-coding RNAs:
Faster sequence search
RNAcentral provides a sequence similarity search that allows one to compare a sequence against a comprehensive collection of non-coding RNA. This functionality was first introduced when RNAcentral was much smaller, and in recent releases the searches were running slower than expected. Now we have rebuilt the sequence search using a scalable cloud infrastructure.
The searches are still powered by nhmmer but now they run in parallel and complete much faster. To test this, we repeated all searches launched in 2019 using the new infrastructure and the average search time decreased from 4.5 minutes to 13 seconds!
The new search features an updated interface. It is now possible to explore the results using the same facets as with the text search. For example, you can narrow down the results to human miRNAs from miRBase in just a few clicks. The results can also be filtered by any keyword, similar to text search.
Try the new search and let us know what you think.
Data updates
The following database have also been updated:
- ENA (141)
- Ensembl (release 98)
- FlyBase (FB2019_05)
- HGNC
- PDB
- RefSeq
- PomBase
Get in touch
As always, all data are freely available on the RNAcentral website, via the API, and in the FTP archive. The next release is scheduled for March 2019. In the meantime, if you have any feedback, please get in touch by email, on Twitter, or by submitting an issue on GitHub. We look forward to hearing from you!