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Designing a primer
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Procedure

  

Open the GUI (graphical user interface) of ApE.  For more info about the input sequence, go to the simulator tab.

Copy a nucleotide FASTA sequence from NCBI. This experiment shows an example with insulin FASTA sequence of Drosophila Melanogaster.

Figure 1: Paste the FASTA sequence

 

 

Now select the sequence. 

Figure 2: Selecting the sequence

 

 

To search for primers, go to  "Tools --> Find Primers".

Figure 3: Searching for primers 

 

 

A window is opened in which the user can change the parameters such as length, melting point, GC content etc. Figure 4 shows the window for changing parameters.

 

Figure 4: User can change the parameters.

 

 

 Click "OK" button to search the primer. Now the results is shown in a new page. Figure 6 shows the results.

Figure 5: Primers found in the input.

 

 

Here if the user clicks on a particular primer, it will show the position of the particular primer in the input. An exaple is shown in figure 6.

Figure 6: Cliking on a particular sequence will show its position in the input sequence.

 

 

 

 

 

 

 

 

 

 

 

 

Cite this Simulator:

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