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In Silico PCR Overview

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 silico PCR tab of the Options Panel: 

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There are the following parameters available:

Forward primer - forward primer.

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Maximum product - maximum size of amplified sequence.

Choosing primers

Type two primers for running In Silico PCR. If the primers pair is invalid for running the PCR process then the warning is shown. Also, primers for the running In silico PCR can be chosen from a primer library. Click the following button to choose a primer from the primers library: 

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  <img src="/wiki/download/attachments/13435073/Primers Library.png"/>
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 The following dialog will appear:  

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  <img src="/wiki/download/attachments/13435073/Primers Library_1.png"/>
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The table consists of the following columns: name, GC-content (%), Tm, Length (bp) and sequence. Select primer in the table and click the Choose button. 

Click the Reverse-complement button for making a primer sequence reverse-complement: 

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  <img src="/wiki/download/attachments/13435069/In Silico PCR_1.png"/>
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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.

 Products table

There are three columns in the table:

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