miRBase

Release of miRBase 20 approaching

by Christoph on June 17, 2013

in miRBase

It has been almost a year since the last miRBase update and according to Sam from miRBase we should see the release of miRBase 20  within this week:

“As you might expect, the extended period since the last release means many new entries — over 3000 new stem-loop sequences, and over 5000 new mature sequences. These additions mostly expand the miRNA sets of species already in the database, rather than adding new species.”

http://www.mirbase.org/blog/2013/06/mirbase-20-is-coming

{ 2 comments }

miRBase Version 19 released

by Christoph on August 1, 2012

in miRBase

miRBase 19As of today, miRBase 19 is available. This latest update features not only the usual additions of sequences and increased coverage of species, but also deletions of over 130 misannotated sequences as well as implementation of the recent changes in the miRNA nomenclature. In detail:

  • 25 new species (mostly plants) are listed. Total number of species is now 193.
  • 3171 new hairpin sequences bring the total number to 21264 precursor sequences.
  • 3625 novel mature products increase the total to 25141 mature miRNAs.
  • 133 entries were removed in this release, many from the rice miRNA complement.
  • A number of cases of duplicate entries mapping to a single genomic locus were cleaned-up.
  • The miR* nomenclature which was partially retired with miRBase 18 is finally retired for all species.

We will add more species specific numbers and changes once we got a chance to dig through the details.
The full README file is available on the official miRBase FTP site, along with downloadable files containing all data in various formats. The official miRBase blog release post can be found here.

 

Incoming search terms for this article:

{ 0 comments }

miRBase 18 Released

by Christoph on November 3, 2011

in miRBase

miRBase 18UPDATE: miRBase version 19 is the current version
********

As 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

Incoming search terms for this article:

{ 4 comments }

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/

{ 0 comments }

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?

Incoming search terms for this article:

{ 0 comments }

miRBase Version 17 Update Released

April 27, 2011

UPDATE: miRBase version 19 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 […]

Read the full article →

miRBase: integrating microRNA annotation and deep-sequencing data

January 10, 2011

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 […]

Read the full article →

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 […]

Read the full article →

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 […]

Read the full article →

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 […]

Read the full article →