miRBase

miRBase 18 Released

by Christoph on November 3, 2011

in miRBase

miRBase 18As promised – miRBase 18 was just released: Release 18 of the database contains 18226 entries representing hairpin precursor miRNAs, expressing 21643 mature miRNA products, in 168 species. As compared to miRBase version 17 a total of 1488 new hairpin sequences and 1929 novel mature products have been added.

Apart from the the usual addition and corrections this release continues to improve adaption of the newer nomenclature: In mirBase version 18 all miR/miR* pairs for mature miRNAs from human, mouse and C. elegans were replaced with the -5p/-3p nomenclature. More species to follow in future releases. For a detailed article about the miRNA nomenclature see: miRBase Nomenclature – a few changes.

A partial list of changes in terms of mature miRNAs:

Acacia auriculiformis -wattle (aau)
7 new sequences

Anolis carolinensis – Carolina anole (aca)
416 new sequences

Arabidopsis thaliana – mouse-ear cress (ath)
62 new sequences, 2 name changes

Ascaris suum – large roundworm of pigs (asu)
416 new sequences

Caenorhabditis elegans – roundworm (cel)
28 new sequences, 247 name changes

Ciona intestinalis – sea squirt (cin)
38 new sequences

Drosophila melanogaster – fruit fly (dme)
4 new sequences, 4 sequence changes, 1 deletion

Glycine max – soybean (gma)
188 new sequences, 12 name changes

Homo sapiens – human (hsa)
190 new sequences, 5 sequence changes, 450 name changes, 2 deletions

Medicago truncatula – Barrel Medic or Barrel Medick or Barrel Clover (mtr)
291 new sequences, 1name change

Mus musculus – mouse (mmu)
48 new mnature miRNAs, 2 sequence changes, 646 name changes, 2 deletions

Oryza sativa – rice (osa)
115 new sequences, 15 name changes, 2 deletions

Oryzias latipes – Medaka and Japanese killifish (ora)
144 new sequences

Rhesus lymphocryptovirus (rlcv)
20 name changes

Rhipicephalus microplus – cattle tick (rmi)
24 new sequences

Sarcophilus harrisii – Tasmanian devil (sha)
65 new sequences

Sorghum bicolor – sorghum  (sbi)
24 new sequences, 1 name change

Sam from miRBase talks about the addition of sequencing data, new features and request user feedback – so, let him know what you think:
http://www.mirbase.org/blog/2011/11/mirbase-18-released/

For the official release notes for miRBase 18 see: ftp://mirbase.org/pub/mirbase/CURRENT/README

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miRBase 18 is on its way

by Christoph on October 31, 2011

in miRBase

According to Sam from miRBase, the next version of the the public database content will be released this week. It will be miRBase version 18. The release will contain 18226 entries representing hairpin precursor miRNAs, expressing 21643 mature miRNA products, in 168 species. That represents 1488 new hairpin sequences and 1929 novel mature products. More numbers when miRBAse 18 gets released…
Sam’s post: http://www.mirbase.org/blog/2011/10/mirbase-18-is-coming/

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miRNA Nomenclature: A Few Changes

by Christoph on April 27, 2011

in miRBase, News

The latest miRBase update to version 17 incorporated also some changes reg. the nomenclature. Sam from miRBase.org did a great job  summarizing the current status as well as the changes they started implementing with version 17. The short version of the changes is:

  • The “*” nomenclature will be retired. In fact, for Drosophila it was retired effective this update and the effected sequences were renamed. Instead of “*” the -3p/-5p nomenclature will be used from now on.
  • The -as/-s nomenclature was retired.

For the full details and additional recommendations check out Sam’s excellent post: “What’s in a name?“

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miRBase Version 17 Update Released

by Christoph on April 27, 2011

in miRBase

UPDATE: miRBase version 18 is the current version
********

Yesterday the latest miRBase Version 17 was released and judging by the numbers this is a rather significant update. This latest release of the microrna database contains 16772 entries representing hairpin precursor miRNAs, expressing 19724 mature miRNA products, in 153 species. There are 1626 new hairpin sequences and 2406 novel mature miR and miR* products that have been added.

Surprising to me personally is the large number of new human miRNA sequences: The number of known unique mature human miRNAs increased by 521 (or 43%) to the current count of 1733 (up from 1212). While only a single new mature rat miRNA is included, there are now 71 new mature mouse miRNA sequences listed in the database. Apart from the additions and corrections there are also more deep sequencing data added.

As usual, the data are freely available to all through the web interface at http://www.mirbase.org/ and in flat file form from ftp://mirbase.org/pub/mirbase/.

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miRBase: integrating microRNA annotation and deep-sequencing data

by Chris on January 10, 2011

in Publications

miRBase is the primary online repository for all microRNA sequences and annotation. The current release (miRBase 16) contains over 15,000 microRNA gene loci in over 140 species, and over 17,000 distinct mature microRNA sequences.

Deep-sequencing technologies have delivered a sharp rise in the rate of novel microRNA discovery. The miRBase curators have mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow us to revisit previous annotations.

miRBase is available online at: http://www.mirbase.org/.

Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic acids research 39(Database issue), D152-57. [article]

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miRBase 16 Released

September 13, 2010

UPDATE: miRBase version 18 is the current version ******** Ok, this one came as a surprise – never got an email from the miRBase mailing list. Still looking through the data – but it’s clear that this update is another BIG one. Not just newly added species but major additions to well characterized species. The [...]

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MicroRNA Expression Analysis

June 3, 2010

Biocompare – Featured Article Wednesday June 02, 2010 – by Jeffrey M. Perkel If you want an inkling of how hot the microRNA field is, just look at miRBase. In April, the University of Manchester’s miRNA database updated to version 15 with the addition of some 4,000 new sequences, including 300 or so new human [...]

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miRBase Growth Turning Exponential

May 25, 2010

After  couple of years with nominal growth in the number of database entries, miRBase growth has turned to exponential over the last four to five updates.  The latest deep sequencing technologies have played a key role in the discovery of new miRNAs.  A full 30% increase in the number of entries and a 48% increase [...]

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miRBase Version 15.0 is Released

April 26, 2010

UPDATE: miRBase version 18 is the current version ******** April 26th, 2010 – miRBase microRNA Sequence Database Updated to Release 15.0 The latest version (15.0) of the miRBase sequence database for known miRNAs was released today. miRBase 15 is freely available at http://www.mirbase.org/. You can find a quick summary for the new release at ftp://mirbase.org/pub/mirbase/CURRENT/README. [...]

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miRBase version 15 approaching

April 21, 2010

Today the official miRBase site announced the upgrade to miRBase 15 over the coming weekend: The long-overdue release 15 of miRBase is expected between 23rd and 26th April, including over 4000 new entries. Cannot wait to see additional sequences for some of the species… Incoming search terms for this article:miRBase 15 ver

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