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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| readme.mkd | 2015-01-21 | 3.4 kB | |
| Protospacer_Workbench.MacOSX.64bit.tar.gz | 2015-01-20 | 46.4 MB | |
| Totals: 2 Items | 46.4 MB | 0 | |
README: Protospacer Workbench
Contents
- About
- Minimum system requirements
- Installation
- Where to find help
- Mailing list
- Contact us
About
Design of guide-RNAs for CRISPR/Cas genome editing system is intuitively easy, but computationally difficult. The main difficulty arises from the need to identify potential off-targets, i.e. possible genomic locations that may be targeted without intention. Current online tools for guide-RNA design provide a user friendly interface to sequence mapping software such as Bowtie or BLAST. However, while fast, these mapping algorithms were not designed with high tolerance to error, a feature critical to determining potential off-targets. Where online tools fail, offline tools for guide-RNA design succeed. However, offline tools require knowledge of the command line which few biologists need/have. Protospacer Workbench aims to bridge the gap between online and offline guide-RNA design. It does so by providing a graphical user interface that allows for the design, analysis, databasing and sharing of guide-RNA designs. The software is designed to facilitate CRISPR use in established genomes and to facilitate establishment of CRISPR for new genomes. Any genome or set of FASTA sequences may be analysed, whether the genome is fully assembled or not. The software is a continuing project and will continue to improve as new advances in guide-RNA design are made. We would therefore like to encourage you to sign up to our mailing list and participate in improving the software by send us your comments and suggestions.
Minimum system requirements
You should have at least a 64-bit computer running Mac OS X 10.7 or above. On OS X 10.7 Some 3rd party mapping tools will not function. We recommend updating to the latest OS X version. Moreover, Cas-offinder is a powerful third-party software package for finding potential guide-RNA off-targets. But, to use Cas-offinder, you need an OpenCL compliant graphics card. Check the following website to see if your machine can run cas-offinder (http://support.apple.com/en-us/HT202823). Please note that it is not essential to be able to run Cas-offinder in order to make use of Protospacer.
Installation
- Download the compressed binary from the Sourceforge project page: https://sourceforge.net/projects/protospacerwb/
- Unpack the downloaded file to somewhere on your hard drive where you have read and write permissions.
- Right-click on the "ProtospacerWB" executable and select "Open".
- Confirm any security question that OS X might ask you.
- If you see the main screen with a white box labeled, "Available databases", then Protospacer Workbench has successfully installed.
- You may now open the program by double-clicking on it, at any time.
Where to find help
The software has context sensitive help built into it. To access this help, simply click on the "Help" button on the bottom left of the screen. Alternatively, you can view the online video tutorials hosted on Youtube by visiting http://www.protospacer.com/support.html.
Mailing list
You can sign up to the main mailing list at http://eepurl.com/XbIVz, or by visiting www.protospacer.com and clicking on the "CONTACT" link.
Contact us
A contact form and our email address is available from http://www.protospacer.com/contact.html. We will make every effort to reply as soon as possible.