26 Feb 2015

RNAcentral release 2

We are pleased to announce the second public release of RNAcentral, which includes the addition of two new Expert Databases (PDBe and snOPY), and a host of new website features and user interface improvements.

New data

  • New expert database: PDBe
    The Protein Data Bank Europe is a member of the Worldwide Protein Data Bank (wwPDB). It provides access to experimentally determined 3D structures of nucleic acids, proteins, and complex assemblies. Now you can explore PDB sequences in RNAcentral or search RNAcentral for your favourite PDB identifier.
  • New expert database: snOPY
    The snoRNA Orthological Gene Database provides comprehensive information about small nucleolar RNAs (snoRNAs), snoRNA gene loci, and target RNAs as well as information about snoRNA orthologues. Explore snOPY data in RNAcentral.
  • Updated ENA dataset based on release 122 and daily updates through February, 17
  • Updated RefSeq dataset
  • Updated human Vega dataset
In total 338,614 new ncRNA sequences and more than 500K additional cross-references have been added to the RNAcentral database since the previous release. The data are available via the website, API or in the FTP archive.

New website features

Species-specific RNAcentral IDs can be used for annotation purposes and allow for contextualised linking to RNAcentral.

  • Search results are now downloadable in fasta, json, or accession list formats.

  • You can also search RNAcentral by literature (author, publication, PubMed ID, or DOI). See examples and the field-specific search syntax on the search help page.
  • There is a new Publications tab, which shows all publications associated with a sequence. For example, searching for “braveheart” finds ncRNA sequence URS00007E3FCE, which is linked to two papers about braveheart:
  • other improvements
    • new search results ranking that puts sequences from key species at the top of the results list
    • keyboard shortcut: press the “/” key to activate the cursor in the search box (just like in Gmail!)
    • better compatibility with older browsers (IE <10).

  • Future plans

    The next RNAcentral release is provisionally scheduled for May 20, 2015. If you would like to get your data into RNAcentral in time for Release 3, please make sure that your data is submitted to us by May 6th.
    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 links below.
    RNAcentral Events public calendar: HTML | XML | iCal

    We need your feedback!

    We are constantly looking for ways to improve RNAcentral, so if you have any questions or feedback please do not hesitate to get in touch by email, engage us on Twitter, or submit a bug report on GitHub.