ftp://mirbase.org/pub/mirbase/CURRENT/README
The miRBase Sequence Database -- Release 14 ------------------------------------------- 0. NEWS The miRBase database has moved to a new location at http://www.mirbase.org/, hosted in the Faculty of Life Sciences, University of Manchester. miRBase in Manchester is now funded by the BBSRC. The miRBase Targets site and pipeline have devolved into the Enright research group at EBI under the name MicroCosm (http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/). All existing URLs should forward to their new locations. Please update your links, and note the new contact email address (mirbase@manchester.ac.uk). The miRBase sequence database has broken through the 10000 entries barrier! 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 14 of the database contains 10883 entries representing hairpin precursor miRNAs, expressing 10581 mature miRNA products, in 115 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 13.0 1367 new hairpin sequences and 1580 novel mature miR and miR* products have been added. See the miRNA.diff file for the full description of changes. Sequences from Daphnia pulex, Phaseolus vulgaris, Malus domestica, Herpes B virus, Brachypodium distachyon, Aquilegia coerulea, Infectious laryngotracheitis virus, Herpesvirus of turkeys, Populus euphratica and Equus caballus are included for the first time. 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 maturestar.fa - minor miR* sequences in fasta format miRNA.dead - entries removed from the database miRNA.diff - differences between the current and last release miFam.dat - family classification of related hairpin sequences The genomes/ directory contains gff files of genome coordinates for, based on the following genome assemblies: aga.gff - A. gambiae (AGAMP3) ame.gff - A. mellifera (AMEL4.0) ath.gff - A. thaliana (TAIR9) bfl.gff - B. floridae (Braf2) bmo.gff - B. mori (SILKDB2.0) bna.gff - B. napus (BrassicaDB-20080411) bta.gff - B. taurus (BTAU4.0) cap.gff - Capitella sp. I (Capca1) cbr.gff - C. briggsae (Wormbase WS200) cel.gff - C. elegans (WormBase WS200) cfa.gff - C. familiaris (CanFam2.0) cin.gff - C. intestinalis (JGI2.0) cre.gff - C. reinhardtii (JGI Chlre3.1) csa.gff - C. savignyi (CSAV2.0) dme.gff - D. melanogaster (BDGP5.0) dps.gff - D. pseudoobscura (DPSE2.0) dre.gff - D. rerio (WTSI Zv8) dsi.gff - D. simulans (DroSim1) eca.gff - E. caballus (EquCab2) fru.gff - F. rubripes (FUGU4) gga.gff - G. gallus (WASHUC2) gma.gff - G. max (JGI Glyma1) hsa.gff - H. sapiens (GRCh37) lgi.gff - L. gigantia (JGI1) mdo.gff - M. domestica (MONDOM5.0) mml.gff - M. mulata (MMUL1.0) mmu.gff - M. musculus (NCBIM37) mtr.gff - M. truncatula (Mt2.0) nve.gff - N. vectensis (Nemve1) oan.gff - O. anatinus (OANA5) osa.gff - O. sativa (TIGR6.0) ptc.gff - P. trichocarpa (Poptr1.0) ptr.gff - P. troglodytes (PANTRO2.1) rno.gff - R. norvegicus (RGSC3.4) sbi.gff - S. bicolor (JGI sbi1) sme.gff - S. mediterranea (WUSTL3.1) tca.gff - T. casteneum (TCAS2.0) tae.gff - T. aestivum (TIGR tae2) tni.gff - T. nigroviridis (TETRAODON8) vvi.gff - V. vinifera (Genoscope 20070911) xtr.gff - X. tropicalis (JGI4.1) zma.gff - Z. mays (TIGR AZM5) ebv.gff - Epstein Barr virus (EMBL:AJ507799.2) hcmv.gff - Human cytomegalovirus (EMBL:X17403.1) kshv.gff - Kaposi sarcoma-associated herpesvirus (EMBL:U75698.1) mghv.gff - Mouse gammaherpesvirus 68 (EMBL:U97553.1) 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 Sequence database is described in the following articles: 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 -- SGJ