| mirbase.db {mirbase.db} | R Documentation |
Welcome to the mirbase.db custom annotation package. This package contains multiple organisms. The purpose is to provide detailed information about the mirRBase microRNA database (http://www.mirbase.org/). In particular, it covers the searchable database of published microRNA sequences and annotation and not the miRBase Registry and Targets database. As requested by the providers of this resource, the references below should be cited when making use of the data. Ambros et al. 2003 provides guidelines on microRNA annotation.
The current version and release date are:
miRBase (Version: 19)
ftp://mirbase.org/pub/mirbase/CURRENT/
With a date stamp from the source of: 01 Aug 2012.
This information is also available by using the
mirbase() function.
This package is updated biannually.
You can learn what objects this package supports with the following
command:
ls("package:mirbase.db")
Each of these objects has their own manual page detailing where relevant data was obtained along with examples of how to use it. Many of these objects also have a reverse map available. When this is true, expect to usually find relevant information on the same manual page as the forward map.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. NAR 2008 36(Database Issue):D154-D158 http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D154
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. NAR 2006 34(Database Issue):D140-D144 http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D140
Griffiths-Jones S. The microRNA Registry. NAR 2004 32(Database Issue):D109-D111 http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D109
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. A uniform system for microRNA annotation. RNA 2003 9(3):277-279 http://www.rnajournal.org/cgi/content/full/9/3/277
ls("package:mirbase.db")