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Videos How to use How to cite

To get you started you can try the following two demo alternatives:

Using the included GeCKOv2 Reference Library:

  1. Choose a GeCKOv2 library, for example the human A+B library.
  2. Copy the content of the demo_input_example.txt file (found here) and paste it in the input box. Alternatively input a number of genes of your interest. Make sure to press enter between each gene.
  3. Press the run button.

Using another Reference Library:

  1. Download the sample Reference Library demo_source_list.txt here.
  2. Upload the demo_source_list.txt under “Upload a Reference Library”.
  3. Set the Gene ID Column to 1 (as the first column of this reference library contains the Gene IDs).
  4. Set the gRNA Column to 2 (as the second column of this reference library contains the gRNA sequences).
  5. Download an example of a typical input query demo_input_example.txt here.
  6. Copy the content of the demo_input_example.txt file and paste it in the input box.
  7. Press the run button

Note:The sample Reference Library (demo_source_list.txt) file contains only a few genes and cannot be used to designing a functional library as the gRNA sequences and scores are random.

Reference Library

Detailed Information

Doench JG*, Fusi N*, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J*, Root DE*. (Corresponding authors *)
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.
Nat Biotechnol. 2016 Feb;34(2):184-91. doi:10.1038/nbt.3437. Epub 2016 Jan 18.

Upload a Reference Library | info

Format: Tab Delimited Text File.

Gene ID Column
gRNA Column
Rank Column (optional) Use Ranking

Enter the genes to query. Press Enter after each one.

Allow for partial matches

Row count: 0

Ranking Order:
Limit to top:
5' Bases
3' Bases

Syntax: {Name}:{Sequence}




Columns to use for the compact output:
Output file name:

This project was financially supported by the Swedish Research Council, the Swedish Foundation for Strategic Research, the Wenner-Gren Foundations, the Jeanssons Foundations, BILS (National Bioinformatics Infrastructure for Life Sciences), and the Karolinska Institutet.

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