Genome Analysis Software Site

in silico biology, inc.

IMC i02 P03 Primer Design Covering Whole Genome with Products

Product · Edition



Design primer sets that amplify all designated features present on the genome sequence.

It can be designed avoiding the place where specified feature such as repeat site exists.

In addition to the whole genome, design range on the genome can be specified.

For the range information of features to be used for designing, use the Feature Key search result file.

You can select the following as the design condition.

A primer set including a specified base range and designed to the outside

A primer set designed inside the designated base range

Repeat design can be executed while loosing conditions for nucleotide sequence regions that could not be designed under the previous design conditions.


Load the template genome base sequence into the current main directory (from Ver.5.2).

Select Menu -> Search -> FK Search ....

The Feature Key Search diary is displayed.

Check the feature key to specify the range to be amplified and specify it.

Multiple designation is possible, but it is desirable to choose only one kind.

If you want to target only features within a genome, specify the range in which the target feature exists in From To.

By default, the whole genome range is specified.

Click Set.

The Feature Key Search Result window is displayed.

the target feature.

Please refer to FK Search for detailed operation method of Feature Key Search Result window.

After selecting, click CSV.

The Save File dialog will be displayed.

Save the CSV file with an arbitrary name.

Select Menu -> Cloning -> Batch Primer Design.

The Batch PCR Primer Design dialog is displayed.

Click Ref ... to specify the CSV file created by Feature Key Search.

Click Parameter. In this section, we will explain only the parameter settings important for bulk design.

Batch PCR Primer Design Parameter Setting Dialog Box will be displayed.

To design outside, click the Outside radio button.

When designing it outside, designate the designable range by counting the number of bases on the upstream side with the nearest base outside each feature being 1.

For example, if you want to design the Forward Primer in the range from 200 bases upstream to the 101 bases position of the feature, set the Primer Design Range (Extra Upstream Bases) to 200 and 101.

Likewise for Reverse Primer, set Primer Design Range (Extra Downstream Bases) to 101 and 200.

Click the Inside radio button to design it inside.

When designing it inside, set the minimum amplification base length (Min. Amplify Length).

Click Find Primer Pair ... (Design Primer).

Processing time is required when targeting the entire genome.

A progress message is displayed during design process execution.

When execution is completed, the Primer List window will be displayed.

The number of primer pairs designed for each feature's position is displayed on the left panel. For the position where the count is 0, it means that the primer set could not be designed under the given design conditions.

Check the line whose count is not 0 out of the design position (feature position) of the left panel.

The list of primer pairs designed for the selected line (corresponding to the feature position) is displayed for the count number.

Click the Select the Best Primer Pair in the lower right.

The best primer pair is checked.

If multiple lines are checked on the left panel, the optimal primer pair is selected for each checked line.

Save as a (New) Click Primer.

The checked primer pair is registered in My primer set.

Click on CSV ..

The checked primer pair is output as a CSV format file.

Click Insert New Feature.

The priming site of the checked primer pair is registered in the current feature map as a new feature Primer.

Full-Text Search the Site

(Under Construction)

Recent Updates (Solution)