4 Jun 2015

RNAcentral release 3

We are pleased to announce that the third public release of RNAcentral is now available. It includes three new Expert Databases (SGD, TAIR, and WormBase), new sequence search powered by nhmmer and many user interface improvements.

New Expert Databases

  • SGD is a database for the budding yeast that provides comprehensive integrated biological annotations.
  • TAIR is a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana
  • WormBase curates, stores and displays genomic and genetic data about nematodes with primary emphasis on C. elegans and related nematodes

Updated data

Five Expert Databases received updates in this release:
  • ENA
  • PDBe
  • RefSeq
  • snoPY
  • Vega
Over 160 thousand new ncRNA sequences and more than 1.1 million additional cross-references have been added to the RNAcentral database since the previous release. You can access the data via the website, API, and the FTP archive.

New website features

New sequence search

The sequence search is now powered by nhmmer which is more sensitive and returns more hits than Exonerate. Also there are several new features:
  • search results have stable URLs and can be accessed up to 7 days after the search is finished
  • results are sortable by E-value, sequence identity, and query/target coverage
  • exact sequence matches are looked up instantaneously and the search can be cancelled if the exact sequence match is all you needed
  • search can be initiated by a URL with the following format:
    http://rnacentral.org/sequence-search?q=<RNAcentral ID>, for example:

Search with ontology terms

Gene Ontology, Sequence Ontology, and Evidence Ontology terms provided by Expert Databases are now searchable.
For example, here are all entries annotated with Gene Ontology term GO:0005840 (ribosome): http://rnacentral.org/search?q=GO:0005840
More ontology terms will be added and additional functionality will be implemented in the future releases.

Other improvements

  • sequence length distribution graph can be used for launching searches:
  • most internal transcribed spacer sequences have been removed from the ENA Noncoding product and are marked as obsolete in RNAcentral.
    You can browse obsoleted sequences using the RNAcentral search.
  • Rat and Zebrafish sequences are now mapped onto the latest genome assemblies (Rnor_6.0 and GRCz10 respectively)

Planning for Release 4

The next RNAcentral release is provisionally scheduled for September 16th, 2015. If you would like to get your data into RNAcentral in time for Release 4, please make sure that your data is submitted to us by September 1st

RNAcentral maintains a public Events calendar, which will be updated if the release dates need to be adjusted. You can subscribe to the calendar using the following links: HTML | XML | iCal

ncRNA Online Databases Training Course

There is still time to register for a one day training course that will give an overview of RNAcentral, miRBase, Rfam, and GENCODE. The developers of these four ncRNA databases will demonstrate how to use these resources to their full potential and lead interactive hands-on sessions. The course will be held on June 17th at the EMBL-EBI campus near Cambridge, UK.

Get in touch

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!