6 Jan 2017

RNAcentral release 6

To kick off 2017 we are happy to announce that a new version of RNAcentral is now available. The latest release includes official human gene names from the HGNC database as well as new data from ENA, RefSeq, and PDB. The data are available on the RNAcentral website, via the API, and in the FTP archive.

Official human ncRNA gene names from HGNC

Starting from this release, RNAcentral links to ncRNAs from HGNC, which is a database that assigns unique and stable names to human genes. The HGNC gene symbols are the official names for human genes and are widely used in the literature and across many resources. You can find out more about HGNC in this NAR paper.

In addition to gene names, HGNC provides manually curated links to relevant publications and database accessions from RefSeq, Vega, and other resources. We used these accessions to map HGNC identifiers to RNAcentral entries so that each HGNC entry is matched to one RNAcentral sequence. For example, the HGNC entry for HOTAIR corresponds to RefSeq accession NR_003716, which is found in RNAcentral under the identifier URS000075C808.

As a result of this mapping, over 95% of 6,357 HGNC ncRNA genes of the sequences were connected to RNAcentral identifiers using RefSeq, Vega, or gtRNAdb identifiers from HGNC. If none of these were found in RNAcentral, we retrieved sequences for Ensembl genes (where available) using Ensembl REST API and matched them to RNAcentral accessions by sequence identity. Only about 300 HGNC ncRNA entries (<5%) remained unmapped, most of which are piRNA clusters, rRNAs, and snoRNAs. Some of these ncRNAs will be matched to RNAcentral in future releases, as they get integrated in RefSeq and other RNAcentral databases. Other RNAs, such as piRNA clusters, are unlikely to be mapped to RNAcentral because they correspond to a large number of RNA sequences.

Browse ncRNAs from HGNC or view HGNC summary page in RNAcentral.

Database growth over time

RNAcentral now contains almost 11 million unique RNA sequences from 23 Expert Databases. There are 750 thousand new distinct ncRNA sequences and 2 million additional cross-references from ENA, PDB, RefSeq in release 6 compared to release 5. To see how the RNAcentral database grew over time, explore the interactive charts at the RNAcentral stats page.

New NAR paper

If you haven’t seen the latest RNAcentral paper, the final version was published in the 2017 Database Issue of Nucleic Acids Research.

Get in touch

We plan to make the next release available in March, 2017. In the meantime, if you have any feedback please feel free to get in touch by email, on Twitter, or by submitting an issue on GitHub. We look forward to hearing from you!

1 Nov 2016

New paper is out

new RNAcentral paper has been published in Nucleic Acids Research as part of the 2017 Database issue. The paper gives an overview of activities over the last two years since the first RNAcentral release and shows examples of how RNAcentral is used in the wild.

Read the paper at the NAR website and feel free to get in touch with any comments or feedback.

26 Sep 2016

Workshop: Databases for miRNA and lncRNA Biology

Have you ever struggled to find sequences for a non-coding RNA that you read about in a paper? Or have you tried to reconcile conflicting ncRNA annotations from different sources? If so, then this half-day workshop might be for you.

Update: Course notes are now available.

3 Aug 2016

New online training course

Are you interested in RNAcentral but don't know where to start? Do you want to see all the website features in action? A new online training course shows how to use RNAcentral and gives tips for efficiently searching the data.
Also in the course:
  • how to browse ncRNAs by genomic location
  • how to submit data to RNAcentral
  • hands-on exercises and an interactive quiz
Take the course and feel free to let us know if you have any feedback.

30 Jun 2016

Join the RNAcentral team

Are you passionate about RNA bioinformatics and experienced with RNA structure and genome browsers? Or are you an expert Web Developer thinking about applying your skills to bioinformatics? Look no further, as we have open positions for a Bioinformatician and a Web Developer to take RNAcentral to a new level.
Funded by BBSRC, the next phase of RNAcentral development will involve importing new types of data such as RNA secondary structure and RNA modifications, connecting sequences to reference genomes, and developing new visualisations for displaying this information in a user friendly way.
Read full job descriptions and apply now:
If you know someone who might be interested in these vacancies, please help us spread the word.