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Figure 4 | Plant Methods

Figure 4

From: An easy-to-use primer design tool to address paralogous loci and T-DNA insertion sites in the genome of Arabidopsis thaliana

Figure 4

Integration of the primer design tool in SimpleSearch. There are three ways to enter the primer design tool in SimpleSearch: (i) via the navigation menu following the link “GK primer design”; (ii) via a link from an insertion prediction (“go to primer design”) that leads directly to the respective insertion position; (iii) via a button in the visualisation (“go to primer design”) for the current central position. The target position for the primer design can be chosen in the user interface by using the chromosomal position according to the TAIRv10 genome sequence (“Jump to position …”), or by using the AGI code of the gene of interest (“Jump to gene code …”) (1); primer sequences are listed at the bottom as well as their positions (2); the annealing temperature and desired distance to the target position can be specified (3); primer design is initiated by using the respective button, after one primer pair has been designed additional primer pairs can be made using the button right to it (4); primer pairs are shown in the visualisation, when more than one primer pair has been computed the one generated last is shown here (5); the amplimer size for the designed primers is shown, as well as possible primer combinations for genotyping, which are accessible via a mouse-over window when GK insertion predictions are spanned by the amplimer (6).

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