SDM-Assist is a stand-alone application which allows SDM primer design in just 3 clicks without the need for an internet connection and will work on almost any Mac/Windows machine.
For a detailed description please refer to our paper : (Journal Page)
Software license: [CC BY-NC-ND]
SDM-Assist is available free of charge for non-commercial use. For non-academic use, contact authors for permission. When publishing data generated resulting from use of the software, please cite:
Karnik A, Karnik R and Grefen C: SDM-assist software to design site-directed mutagenesis primers introducing “silent” restriction sites. BMC Bioinformatics 2013, 14:105; DOI: 10.1186/1471-2105-14-105
For enquiries and further information about SDM-Assist, please e-mail firstname.lastname@example.org
OTHER THINGS YOU NEED TO KNOW
*Allows the user to generate and choose primers for SDM that contain a unique restriction site identity allowing for highly efficient identification of ‘mutated clones’ by a simple restriction digest.
*Suggested primer pairs are scored based on factors such as Tm, GC content, 5 prime and 3 prime-stability and secondary structure.
*Ability to custom choose and feed restriction enzymes to SDM-Assist for inserting silent restriction sites in the primers.
*All suggested primer sequences along with detailed information on them can be exported into an excel or text file.
*A useful reference tool in the display window of the programme, which logs the sequence of events and provides brief tips as you design the primer.
1. Installing the Adobe AIR package: If Adobe AIR is not installed on your machine you will be asked to install it first. Clicking the image will take care of AIR installation.
2. Installing SDM-Assist: After step 1 (or if AIR is already installed), SDM-Assist will be installed. You will be prompted to “Open” or “Save” the file. Select “Open” to proceed with installation.
3. In the options screen, you will be asked if you want to create a desktop icon. Please check this box so that the application icon is available on the desktop.
4. Uninstalling SDM-Assist: To uninstall from Windows, Go to Control Panel>Uninstall Program and select SDM-Assist. Click ‘Uninstall’/’Remove’ to remove the application. Note: If you get an Error #2032, try clearing the History cache and cookies on the browser. Alternately try using another browser (application not new window) to install the SDM-Assist.
SDM-Assist allows you to customize the list of restriction enzymes used by it. To use a compatible file (tab separated RE Name and RE Sequence, one per line), simply drag n drop it onto the scissors icon.