24 Mar 2016

RNAcentral release 5

RNAcentral and Rfam are in sync

Rfam was integrated into RNAcentral since the first release; however, some Rfam families including small and large ribosomal subunits were not submitted to RNAcentral until now. Starting with this release you can explore all Rfam data in RNAcentral and use RNAcentral export functionality to download the sequences for further analysis. The only Rfam families that will not be found in RNAcentral are lncRNA conserved regions and cis-regulatory Rfam families which do not represent complete ncRNA sequences.
We also fixed the cases where the same region could be annotated by multiple Rfam families from the same Rfam clan. Now only the best scoring annotation is kept, which reduces redundancy and makes the results more consistent. For example, if a human SRP sequence matches both Protozoan and Metazoan SRP families, only the human SRP annotation is kept.

More relevant search results

Up until now search results listed unique sequences, for example, search results for hsa-mir-21 looked like this:
Although the query was a human miRNA, the results linked to pages for 3 distinct sequences that came from multiple species. Now the results link directly to the human entries:
Starting with this release, species-specific entries are the default view in search results.

Data updates

Several databases were updated:
  • NONCODE data was updated from v4 to NONCODE 2016 (human, mouse and gorilla)
  • Vega/GENCODE updated to v63 (human and mouse)
  • the latest data was imported from ENA, RefSeq, and PDB

Genome browser

If you are interested in a certain genomic location, you can find all its non-coding RNAs by using the new Genome browser that puts RNAcentral sequences in context of genes and transcripts from Ensembl and Ensembl Genomes.

Get in touch

As alway, feel free to get in touch by email, on Twitter, or by submitting an issue on GitHub. We look forward to hearing from you!