Team:Arizona State/Project/Software

CRISPR information panel of the CRISPRstudio

We have developed a tool to assist in the development of synthetic CRISPR systems.

• Pick spacers from a source sequence, based on homology with the target genome, hairpinning potential, restriction sites, and known PAMs.
• Output arrays with various formats based on generated spacers.
• Display and gather CRISPR information using a database cultivated from several sources.

Downloads

• Python source: [http://code.google.com/p/crispr-studio/ CRISPRstudio at GoogleCode]

• See Source for details.

• Executable: [http://code.google.com/p/crispr-studio/downloads/detail?name=CRISPRstudio-r52b-win.zip Windows]

• Dependencies: BLAST+ 2.2.25 or compatible.

Installation

Using the provided binaries is the fastest way to get started with CRISPRstudio. Visit our GoogleCode page and select the downloads tab. Download the appropriate build based on your OS. All builds are provided for x87 platforms. For x64 real support, you will need to run the source directly. x64 support has not shown significant speed increases for CRISPRstudio.

Extract the compressed file to some location. You also need to download BLAST+ 2.2.25 or compatible. BLAST+ must be installed and included in the system path. On most systems, the BLAST+ installer will take care of this. After this, you may run MainFrame to start the program.

Source

• The source code is available on our [http://code.google.com/p/crispr-studio/ GoogleCode] page. It is available as a package of the latest revision and directly from Subversion.

• Dependencies: [http://biopython.org/wiki/Download BioPython] 2.7.2 or compatible, [http://new.scipy.org/download.html NumPy] 1.6.1 or compatible, [http://www.wxpython.org/download.php WxPython] 2.8 or compatible, BLAST+ 2.2.25 or compatible

Pick os/arch as needed. Note that each of the python packages should list the version of Python they support - select the right one. NumPy must be installed before BioPython. The x64 release of wxPython doesn't seem to like Win7 so it may be better to use the x86 release. BLAST+ must be included in the system path. If BLAST+ is not available in the the system, the spacer creator will not function. The information browser will still function normally.

The code itself is not fully documented. However, the code was intentionally written to be readable without comments. Project files are available for PyCharm 1.6.

You may then run MainFrame.py to start the program.

Interface

Data Sources

• [http://crispr.u-psud.fr/crispr/ CrisprDB]
• [http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi JCVI CMR]
• [http://crispi.genouest.org/ CRISPI]
• NCBI