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

        Toolbox | Microarray and Small RNA | Small RNA Analysis (Image small_rna_folder) | Download miRBase (Image 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 Information on the version number of miRBase is also available in the History (Image history_16_n_p) of the downloaded sequence list, and when using this for annotation, the annotated samples will also include this information in their History (Image history_16_n_p).

Importing the miRBase data file

You can also import the miRBase data file directly into the Workbench. The file can be downloaded from

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
DE Caenorhabditis elegans let-7 stem-loop
FH Key Location/Qualifiers
FT miRNA 17..38
FT /product="cel-let-7-5p"
FT miRNA 60..81
FT /product="cel-let-7-3p"
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
DE Caenorhabditis elegans lin-4 stem-loop
FH Key Location/Qualifiers
FT miRNA 16..36
FT /product="cel-lin-4-5p"
FT miRNA 55..76
FT /product="cel-lin-4-3p"
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: Once you have created the file, it has to be imported as described above.