You can also download standalone version of Cas-Designer!

To download and run Cas-Designer, please follow below instructions.

STEP 1

Cas-Designer requires the following:

• The latest version of Cas-OFFinder. Please download Cas-OFFinder, follow the instructions here.
• Cas-OFFinder bulge, a small wrapper script for Cas-OFFinder written in Python. You can download it from here.
• Python. If you are using Linux or Unix (such as Max OS X), python is pre-installed and you don't have to install it again. Otherwise, you should download Python from its official website and install it. You can choose either 2.x or 3.x.

NOTE: It is reported that Cas-OFFinder sometimes hangs with certain version of AMD driver due to unknown reason. If you experience this issue, then please try older version of Cas-OFFinder, or use Cas-OFFinder on the system with GPUs/accelerators of other vendors. We are currently examining this issue, and we will release revised version of Cas-OFFinder as soon as we fix it.

STEP 2 - Download and Install

Please download the standalone Cas-Designer script from here. Put it anywhere you want.

In order to run Cas-Designer properly, Cas-OFFinder and Cas-OFFinder bulge should be accssible from anywhere. In order to do that, you need to add the path of both Cas-OFFinder binary and Cas-OFFinder bulge script in PATH environment variable.

How to set PATH (on Linux or Unix):

• Open '~/.profile' or '~/.bash_profile' (existing one) with any editor you want.
• Add following line (change the path to the appropriate one):
  • export PATH=$PATH:/path/to/cas-offinder
• Add following line again (change the path to the appropriate one):
  • export PATH=$PATH:/path/to/cas-offinder-bulge
• Logout and login, or reboot your system. Done.

How to set PATH (on Windows):

• Go to 'Control Center'. Click on 'System'.
• On the left sidebar, Click on 'Advanced System Settings'.
• Click on 'Environment Variables...' button.
• In 'User defined variables' list, find 'PATH' (case insenstive) and select it, and click on 'Edit...' button. If you can't fine one, click on 'Create new...' button.
• Ensure that the variable name is 'PATH'. Do not remove the variable value, just append one semicolon and the path of Cas-OFFinder binary. And then, append one semicolon again, and add the path of Cas-OFFinder bulge script. Click 'OK'.
• Click on all of the remaining 'OK' buttons. Done.

STEP 3 - Usage

Basic Usage:

In order to run Cas-Designer easily, you should create a configuration file.

• The first line is path of target sequence files of any organism, in FASTA or 2bit format.
• The second line is path of input sequence file in FASTA format.
• The third line is crRNA length of targets, without PAM sequence. For SpCas9, it is usually 20.
• The forth line is PAM sequence. Mixed bases are allowed. Example patterns are shown below:
• SpCas9: NGG or NRG
• StCas9: NNAGAAW
• NmCas9: NNNNGMTT
• The fifth line is PAM pattern in target organism. This pattern can be different from the third line's one, but the length should be the same.
• The sixth line is Mismatch number.
• The seventh line is DNA bulge size.
• The eighth line is RNA bulge size.

Example (SpCas9, mismatch number 5, DNA bulge size 2, RNA bulge size 2):

Finally on command-line, you can run Cas-Designer script like below.