27 Nov 2015

RNAcentral release 4

We are pleased to announce that the fourth release of RNAcentral is now available. It includes seven new Expert Databases and RNA modifications from PDBe and Modomics. The data are available on the RNAcentral website, via the API and in the FTP archive.

New Expert Databases

Seven new Expert Databases have been imported in release 4:

RNAcentral summary page
Database description
a model organism database for the social amoeba Dictyostelium discoideum
all non-coding RNAs from Dictyostelium discoideum
a full-length 16S rRNA gene database that provides a curated taxonomy based on de novo tree inference
all sequences from the most recent Greengenes release
an online repository of lncRNA transcripts and annotation
high-confidence human dataset
a database of RNA modifications
tRNA and rRNA modifications
an integrated database of non-coding RNAs
human ncRNAs from NONCODE v4
a comprehensive database for the fission yeast Schizosaccharomyces pombe
all ncRNA sequences
a comprehensive resource for quality checked and aligned ribosomal RNA sequence data
SILVA v122

Five Expert Databases were updated with new data (ENA, PDBe, RefSeq, snoPY, and Vega).

This release brings the total number of imported databases to 22, with more than 15 databases still to be integrated. Have a look at the entire list of RNAcentral Expert Databases and let us know if your favourite ncRNA database is not on the list.

Modified nucleotides

RNAcentral now displays modified nucleotides for sequences from Modomics and for sequences from PDB with modified nucleotides. For example, here is a tRNA from E.coli with modified nucleotide annotations from both databases. To view modifications, just click the View modifications button and the modified nucleotides will be shown on top of the RNA sequence. Here is a quick demo:

In future releases we plan to import more information about RNA modifications and add the ability to search for sequences with modified nucleotides or for sequences with specific types of modifications.

Database growth over time

RNAcentral now contains over 9.3 million unique RNA sequences from 22 Expert Databases. Over 700,000 distinct ncRNA sequences and 7.4 million additional cross-references have been added to the RNAcentral database since release 3.

You can explore the interactive graphs with various database statistics on the about RNAcentral page.

RNAcentral Webinar

Thanks to everyone who tuned in to the first RNAcentral webinar, but if you missed it and would like to catch up, check out the video and the slides from the webinar, as well as a summary of the Q&A session.

Planning for Release 5

The next RNAcentral release is provisionally scheduled for March 2nd, 2016. If you would like to get your data into RNAcentral in time for Release 5, please make sure that your data is submitted to us by February 17th.

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 these: HTML | XML | iCal

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!