miRNA count: 38589 entries

The miRBase database provides a searchable online repository for published microRNA sequences and associated annotation.  miRBase also provides a gene naming and nomenclature function in the miRBase Registry.

Release 22 of the database contains 38589 entries representing hairpin precursor miRNAs, expressing 48885 mature miRNA products, in 271 species.  The data are freely available to all through the web interface at http://www.mirbase.org/ and in flatfile form from ftp://mirbase.org/pub/mirbase/.

10031 new hairpin sequences and 13149 new mature products have been added, an increase in the number of sequences of over a third.  The first miRNAs in 48 new species are reported.  115 hairpins and 496 mature sequences have changed names; the overwhelming majority of these changes are additions of lettered or numbered suffixes to differentiate related loci.  87 misannotated and duplicate sequences have been deleted.  See the miRNA.diff file for the full description of changes.

The “high confidence” microRNA dataset (as described in Kozomara and Griffiths-Jones, NAR 2014) is available on the FTP site.

from the miRBase Blog by Sam & Ana

After repeated and unreasonable delay, miRBase 22 is finally released. As you might expect with such a long gap, the number of sequences in the database has jumped significantly — by over a third. The vast majority of the increase comes from new microRNA annotations in species not previous represented in the database. Indeed, there are sequences for 48 new species in this release. Still, we know we are missing microRNA annotations that have been published. We apologise for that, and will be working hard to catch up and get back to more timely data releases. Please let us know if we are missing your data.

Other new things:

    • We’ve changed how we collect and manage the deep sequencing datasets that you can see in the miRBase read views. The number of deep sequencing datasets that we have mapped has jumped in this release — to 831. We have around 1000 more datasets mapped and ready to go, but we’ve hit a technical issue with database size and speed for the website, for which we didn’t want to hold up the release any further. As soon as we’ve fixed that problem, the deep sequencing data views in miRBase will expand dramatically. With that update, we expect the number of microRNA annotations that will be classified as “high confidence” to also jump significantly.
    • We’re developing interfaces to keep track of the changes in miRBase over time. The first view of that is available in miRBase 22 — click the “change log” links on the microRNA entry pages to see.
    • We’re also developing views of functional data, incorporating both literature mining, and the excellent work of Huntley et al. (RNA 2016 22:667-676). The first views of that will appear on the microRNA entry pages shortly.
    • Look out for a programmatic webservice to retrieve sequences, also coming shortly.

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