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miRBase 21 was published June 26, 2014 and was still in its growth phase. Why is it not being updated anymore or the project declared officially dead? ENSEMBL also uses miRBase as a starting point (http://www.ensembl.org/info/genome/genebuild/ncrna.html).

What do people use now as a good reference for miRNAs especially for less well annotated/sequenced species?

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  • $\begingroup$ Hi Ido Tamir, welcome to Bioinformatics Stack Exchange, and thanks for your question. The Stack Exchange community tries to encourage the asking of specific questions that can have definite, objective answers. It would be appreciated if you could modify your question to fit this format, either by adding more context/story around why you're asking the question, or by reducing the open-endedness of the question. Bioinformatics is a very large subject area, and there are frequently many different ways to do the same thing. $\endgroup$
    – gringer ♦
    Commented Jun 7, 2017 at 12:46
  • $\begingroup$ what part is unspecific in asking for an up to date miRNA database? You mean I should specify that the last update should have been on the 5. june 2016? $\endgroup$
    – Ido Tamir
    Commented Jun 7, 2017 at 16:10
  • $\begingroup$ A quick internet search for me returns at least 4 different databases in the first page: 1 -- miRBase; 2; 3; 4. This is a very common occurrence in bioinformatics, where multiple solutions are created to solve very similar problems. The particular database that is used will depend on your particular application, as each will have their own strengths and weaknesses (e.g. a tradeoff between sensitivity and specificity). $\endgroup$
    – gringer ♦
    Commented Jun 8, 2017 at 6:08

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miRbase is a database of miRNA sequences, their genomic locations and the evidence for their existence. It is not a database of their targets, so I am assuming that this is the information you are asking for.

Despite not having been updated since 2014, as far as I am aware miRBase is still the go to place for this data. For example, courses at the European Bioinformatics Institute were still teaching the use of miRBase in April this year (2017).

RNACentral is repository for all non-coding RNAs, but as it is a synthesis of other databases, including miRBase, I suspect data their will still be largely the same as miRBase.

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If you are still interested, last year miRBase generated new updates. Currently, according to ftp site the last release is 22.1. So, it is not a dead project and for more specific information you should reference the miRBase blog. In order to get the best set of miRNA annotations, you have to define your target species or even if exists some related annotated species and then, retrieve the current annotation along different miRNA databases, but most importantly you have to be really clear about the definition of miRNA families, because it is clearly different in miRBase and also in RFAM.

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I mostly use TargetScan predictions. But here are few curated databases:

  • miRGate

    miRGate is a curated database of human, mouse and rat miRNAs/mRNAs targets. It is designed to analyze miRNA and gene isoforms lists under a common and consistent space of annotations. Including all existing 3 UTR and the entirely known miRNAs. All Havana biotypes and ENCODE principal isoforms for the three organisms are also included. Publication

  • miR2Disease :

    a manually curated database, aims at providing a comprehensive resource of miRNA deregulation in various human diseases. Publication

  • PASmiR

    PASmiR, a literature-curated and web-accessible database, was thus developed to provide a solid platform for the collection, standardization, and searching of these miRNA-stress regulation data in plants. Publication

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For miRNA precursor predictions in species in Ensembl but not in miRBase, you can have a go to MapMi (http://www.ebi.ac.uk/enright-srv/MapMi/) .

You can easily run it locally for other species or if you have smallRNA sequencing done on something new.

Let me know if you run into difficulties or have ideas to improve it.

Ensembl itself has its own miRNA predictions.

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I would guess DIANA-Tarbase ( evidences, https://www.ncbi.nlm.nih.gov/pubmed/25416803 ) and TargetScan (predictions, https://www.ncbi.nlm.nih.gov/pubmed/26267216 ) are good starting points.

Especially for the less annotated species, TargetScan might be helpful.

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    $\begingroup$ thank you very much, but I am not interested in miRNA-target predictions or interactions but a curated database of miRNAs (-5p/-3p , precursor, genomic location, families). targetScan - i think - also relies on miRBase. Still one vote for the effort. $\endgroup$
    – Ido Tamir
    Commented Jun 7, 2017 at 10:21
  • $\begingroup$ It seems that TargetScan uses more miRNAs than those in miRBase (see FAQ number 11: targetscan.org/faqs.Release_7.html). $\endgroup$
    – bli
    Commented Jun 8, 2017 at 9:19

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