DOI: 10.5281/zenodo.3502295
title: The miRBase release 22 reference files: stem-loop sequences (hairpins) and mature miRNA sequences

description: <pre>The miRBase Sequence Database -- Release 22 ------------------------------------------- 1. SUMMARY 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/. 2. CHANGES SINCE RELEASE 21 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. 3. FILES The following files are available from the above ftp site: miRNA.dat - all entries in (almost) EMBL format hairpin.fa - predicted miR stem-loop sequences in fasta format mature.fa - mature sequences in fasta format miRNA.dead - entries removed from the database miRNA.diff - differences between the current and last release The genomes/ directory contains gff files of genome coordinates for 152 species. See the individual files for the genome assemblies used. The database_files/ directory contains dumps of the MySQL relational database that is used to generate the web pages. The documentation for this subset of files is non-existent - use at your peril! 4. LICENSE miRBase is in the public domain. It is not copyrighted. You may freely modify, redistribute, or use it for any purpose. See ftp://mirbase.org/pub/mirbase/CURRENT/LICENSE for details. 5. HOW TO CITE THE miRNA DATABASE The miRBase database is described in the following articles: miRBase: annotating high confidence microRNAs using deep sequencing data. Kozomara A, Griffiths-Jones S. Nucleic Acids Res. 2014 42:D68-D73 miRBase: integrating microRNA annotation and deep-sequencing data. Kozomara A, Griffiths-Jones S. Nucleic Acids Res. 2011 39:D152-D157 miRBase: tools for microRNA genomics. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. Nucleic Acids Res. 2008 36:D154-D158 miRBase: microRNA sequences, targets and gene nomenclature. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. Nucleic Acids Res. 2006 34:D140-D144 The miRNA Registry. Griffiths-Jones S. Nucleic Acids Res. 2004 32:D109-D111 Please cite us if you use the data we distribute, but also be sure to cite the primary sources of miRNA sequences in your work. Guidelines to miRNA annotation are published here: A uniform system for microRNA annotation. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T. RNA 2003 9(3):277-279 Criteria for annotation of plant MicroRNAs. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK. Plant Cell. 2008 20(12):3186-3190 6. FEEDBACK Any queries about data, web services, naming requests or other feedback should be directed to mirbase@manchester.ac.uk. 7. HISTORY Version Date Entries 1.0 12/02 218 1.1 01/03 262 1.2 04/03 295 1.3 05/03 332 1.4 07/03 345 2.0 07/03 506 2.1 09/03 558 2.2 11/03 593 3.0 01/04 719 3.1 04/04 899 4.0 07/04 1185 5.0 09/04 1345 5.1 12/04 1420 6.0 04/05 1650 7.0 06/05 2909 7.1 10/05 3424 8.0 02/06 3518 8.1 05/06 3963 8.2 07/06 4039 9.0 10/06 4361 9.1 02/07 4449 9.2 05/07 4584 10.0 08/07 5071 10.1 12/07 5395 11.0 04/08 6396 12.0 09/08 8619 13.0 03/09 9539 14 09/09 10883 15 04/10 14197 16 08/10 15172 17 04/11 16772 18 11/11 18226 19 08/12 21264 20 06/13 24521 21 06/14 28645 22 03/18 38589 -- SGJ </pre>