Usage

  • Download and extract csidesigner_v1.0.
  • Open the folder csidesigner_v1.0 and then open JavaApplication1.jar, the user interface will open
  • Give the gene symbol (current annotation in NCBI) in the textfield, tick approapriate parameters and then click submit
  • The siRNA selection program will run and the result will be displayed in the table in the rightside of the interface
  • The program may take 5-8 minutes to run
  • After the result is displayed, any one siRNA can be selected and the off target genes can be viewed by clicking the button ""view off targets" in the bottom of the table
  • A seperate window will open which shows the list of off target gene symbols
  • One or more off target genes can be selected and filtered by clicking the button "filter selected off targets" in the bottom of the list
  • The program will start running again and will display potent siRNAs which does not have the selected off targets
  • In case of small numbers of choice siRNA or no choice siRNA, please refine the parameters to loosen the constraints
  • Apart from showing top scoring siRNAs in the user interface, the program also generates three text files-
    "all potent sirs" contains list of all siRNAs classified as potent,
    "top 30" contains top 30 most potent siRNAs
    and "sir_off" contains list of predicted off-targets for each of the top 30 siRNAs
  • In case of small numbers of choice siRNA or no choice siRNA, please refine the parameters to loosen the constraints