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IMC I02D Batch PCR Primer Design

This function designs the Primer unit which amplifies all assignment features which exist on the genome arrangement, lumping together it.
The specified features such as the repeat chromosome region can design an existing part by avoiding it.
The design area on the genom can be specified except the whole of the genom.
The area information of the feature to use for a design uses Feature Key Search result file.
The following can be chosen as the design situation.
The Primer set which is designed outside, containing a specified base area
The Primer set which is designed inside the specified base area
The iteration design can be executed while the design situation immediately ahead relaxes a terms to the base-sequence area which could not be designed.


This loads a lettering-guide genom base-sequence in the current main directory ( from Ver.5.2 ).
Menu --> Search --> This chooses FK Search...
Feature Key Search Dialog is displayed.
This specifies for feature key to specify amplification object scope, checking.
More than one can be specified but the choice thing is desirable in only one kind.
When making only the feature which is in some area of the genom a candidate, this specifies the area that the feature to make a candidate exists in From To.
All genom areas are specified by the default interpretation.
This clicks Set.
Feature Key Search Result window in computer graphics is displayed.
+ This checks in the feature to make a candidate.
As for the detailed operating principle of the Feature Key Search Result window in computer graphics, refer to FK Search.
This clicks CSV behind the choice.
A file conservation DIALOG is displayed.
This saves CSV file with the arbitrary designation.
Menu --> Cloning --> This chooses Batch Primer Design
Batch PCR Primer Design A DIALOG is displayed.
This specifies the CSV file which was created in Feature Key Search by clicking Ref....
This clicks Parameter.
Here, only an important parameter configuration is described in the huge package design.
Batch PCR Primer Design Parameter configuration DIALOG is displayed.
When designing outside, this clicks Outside radio button.
When designing outside, in the nearest base which is outside each feature, as 1, in the upstream side, this counts the number of the bases and this specifies the design possible area.
For example, when wanting to design Forward Primer at the area from the upstream 200 base geometry of the feature to the 101 base geometry, this sets Primer Design Range ( Extra Upstream Bases ) to 200 and 101.
Reverse Primer, too, sets Primer Design Range ( Extra Downstream Bases ) to 101 and 200 in the same way.
When designing inside, this clicks Inside radio button.
When designing inside, this sets a minimum amplification base chief ( Min. Amplify Length ).
Find Primer Pair... This clicks ( Design Primer ).
When making the whole of the genom a candidate, an operation time is taken.
During design aftertreatment execution, a progress message is displayed.
Primer List window in computer graphics is displayed in the execution when finishing.
The number of Primer Pair which were designed every geometry of each feature on the arm cover, left panel is displayed.
This means that the design situation which was given about the geometry where the coumt becomes 0 could not design a Primer set.
This checks in the line that the coumt is not 0 among the design geometry ( the feature geometry ) of the arm cover, left panel.
The list of Primer Pair which was designed in the chosen line ( this is a correspondence in the feature geometry ) is displayed only about the number of the coumts.
This clicks Select the Best Primer Pair which is in the lower right.
This is checked by best Primer Pair.
When checked in more than one line with the arm cover, left panel, best Primer Pair is chosen every checked horizontal line.
Save as a ( New ) This clicks Primer
Checked Primer Pair is subscribed to My Primer Set.
CSV.. This clicks を.
Checked Primer Pair is output as the CSV format file.
This clicks Insert New Feature.
The priming site of checked Primer Pair is subscribed to the current feature map as new feature Primer.


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