Downloading miRBase
In order to make use of the additional information about mature regions on the precursor miRNAs in miRBase, you need to use the integrated tool to download miRBase rather than downloading it from http://www.mirbase.org/:
Toolbox | Microarray and Small RNA | Small RNA Analysis (
) | Download miRBase (
)
This will download a sequence list with all the precursor miRNAs including annotations for mature regions. The list can then be selected when annotating the samples.
The downloaded version will always be the latest version (it is downloaded from ftp://mirbase.org/pub/mirbase/CURRENT/miRNA.dat.gz). Information on the version number of miRBase is also available in the History (
) of the downloaded sequence list, and when using this for annotation, the annotated samples will also include this information in their History ().
Importing the miRBase data file
You can also import the miRBase data file directly into the Workbench. The file can be downloaded from ftp://mirbase.org/pub/mirbase/CURRENT/miRNA.dat.gz.
In order for the file to be recognized as a miRBase file, you have to select miRBase dat in the Force import as type menu of the Standard Import dialog.
A *.dat file follows the following format:
ID cel-let-7
XX
DE Caenorhabditis elegans let-7 stem-loop
XX
FH Key Location/Qualifiers
FH
FT miRNA 17..38
FT /product="cel-let-7-5p"
FT miRNA 60..81
FT /product="cel-let-7-3p"
XX
SQ Sequence 99 BP; 26 A; 19 C; 24 G; 0 T; 30 other;
uacacugugg auccggugag guaguagguu guauaguuug gaauauuacc accggugaac 60
uaugcaauuu ucuaccuuac cggagacaga acucuucga 99
//
ID cel-lin-4
XX
DE Caenorhabditis elegans lin-4 stem-loop
XX
FH Key Location/Qualifiers
FH
FT miRNA 16..36
FT /product="cel-lin-4-5p"
FT miRNA 55..76
FT /product="cel-lin-4-3p"
XX
SQ Sequence 94 BP; 17 A; 25 C; 26 G; 0 T; 26 other;
augcuuccgg ccuguucccu gagaccucaa gugugagugu acuauugaug cuucacaccu 60
gggcucuccg gguaccagga cgguuugagc agau 94
//
Creating your own miRBase file
If you wish to construct a file yourself to be used as a miRBase file for annotation, this is also possible if you format the file in the same way as the miRBase data file. In particular, the following needs to be in place:- The sequences needs "miRNA" annotation on the precursor sequences. In the Workbench, you can add a miRNA annotation by selecting a region and right click to Add Annotation. You should have a max 2 miRNA annotations per precursor sequences. Matches to first miRNA annotation are counting in
5'column. Matches to second miRNA annotation are counted as3'matches. - If you have sequence list containing sequences from multiple species, the Latin name of the sequences should be set. This is used in the Annotate and merge small RNA samples dialog where you can select the species. If the Latin name is not set, the dialog will show "N/A".