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miRBase 16 and deep sequencing data

It’s taken a while.  miRBase is, after all, more than 8 years old. But we’ve dragged ourselves kicking and screaming into the blogosphere, on the off-chance a miRBase blog might be of some minor interest.  So here you will find, in time, news of miRBase releases, discussion of new features, ideas for future development and more.  All, of course, with questions, discussion, feedback and comment from you!

miRBase 16 has been available for a month or so.  You may or may not have noticed the new interface to view short RNA deep sequencing data mapped to miRNA sequences (see, for example, the dme-mir-282 entry). The patterns of mapped reads allow us to see the diversity of mature miRNA sequences (sometimes called isomiRs) expressed from a given locus.  Read counts, summed over many experiments, act as a proxy for miRNA expression.  We can therefore show the relative abundance of miR, miR* and isomiR sequences.  Reads can be filtered by count, experiment, tissue and stage.  We can also use the read data as detailed evidence for miRNA annotations, and so revisit previous dubious annotations.  A new search interface allows us to search for miRNAs by tissue- or stage-specific expression.  We have so far added reads from just a few datasets imported from GEO, but we’ll be adding many more in the coming weeks and months.  A manuscript describing our approaches for dealing with deep sequencing data has been accepted for publication in the NAR 2011 database issue, so look out for that!

We’re keen to hear what you think, and suggestions for improvements are always welcome, here or by email.

Posted in new features, releases.