SDM-Assist

Site-directed mutagenesis

This is the Github repository for SDM-Assist software which is listed in the research paper "SDM-assist software to design site-directed mutagenesis primers introducing “silent” restriction sites. published in BMC Bioinformatics 2013, 14:105; available at DOI: 10.1186/1471-2105-14-105

The SDM-Assist software:

  1. 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.
  2. Scores suggested primer pairs on factors such as Tm, GC content, 5 prime and 3 prime-stability and secondary structure.
  3. Allows user to customize choice of available restriction enzymes to SDM-Assist for inserting silent restriction sites in the primers.
  4. Exports all suggested primer sequences along with detailed information on them into an excel or text file.
  5. Provides brief tips for primer design, logs the sequence of events as readable text in the display window.

Download Software

To use the SDM-Assist software you will need:

  1. Adobe Air Runtime
  2. SDM-Assist Installer Package

Adobe Air Runtime

(Skip this step if you already have Adobe Air Runtime installed)
Due to events beyond the control of the authors, Adobe Air Runtime is now managed by a third-party entity called Harman International. For sake of simplicity, all relevant installer files are provided here, but you can also get the Air Runtime installer from Harman International https://airsdk.harman.com/runtime

Their website contains the latest state of the runtime and will also provide helpful hints on common installer issues.

If you wish, you can access the installer here also:

  1. Windows Installer .exe
  2. Mac Installer package (.dmg)

SDM-Assist Installer Package

The package is common for both Windows and Mac and can be found here: SDM-Assist Installer

Install instructions

  1. If Adobe AIR is not installed on your machine you will need to install it first. Save the relevant files to your local system and then run the installer.
  2. After step 1 (unless not needed), download the SDM-Assist AIR Package and "Open" it.
  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.

Leave us a comment in case of any issues: a.karnik<at>lancaster.ac.uk

Additional resources

The following resources are available for use as needed:

  1. SDM-Assist Helpsheet PDF
  2. Original Restriction Enzyme List TXT
  3. List of all supported restriction enzymes TXT
  4. Tutorial Video YouTube

TERMS OF USE

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