In silico PCR is used to calculate theoretical polymerase chain reaction (PCR) results using a given set of primers (probes) to amplify DNA sequences.

UGENE provides the In silico PCR feature only for nucleic sequences. To use it in UGENE open a DNA sequence and go to the In Silico PCR tab of the Options Panel: 

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There are the following parameters available:

Forward primer - forward primer.

Reverse primer - on the opposite strand from the forward primer. 

Mismatches - mismatches limit.

Maximum product - maximum size of amplified sequence.

Type two primers for running In Silico PCR. If the primers pair is invalid for running the PCR process then the warning is shown. Click the Reverse-complement button for making a primer sequence reverse-complement: 

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Also, primers can be chosen from a primers library. Click Show primers details for seeing statistic details about primers. 

When you run the process, the predicted PCR products appear in the products table.

There are three columns in the table:

• region of product in the sequence
• product length
• preferred annealing temperature 

 Click the product for navigating to its region in the sequence. 

 Click the Extract product(s) button for exporting a product(s) in a file or use double click for that. 

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