In this part of the tutorial, you will use a template to insert three missing bases (AAA) between positions 24 and 25 of the sequence pbr322.seq.
- Choose Create Insertion from the New Script window on the left, or from the Templates panel on the right. Tips for entering your data appear in the yellow “comments” section above the template.
- In the Sequence File area, press the Choose Sequence(s) button.
- Navigate to the extracted tutorial data folder and double-click on pbr322.seq.
- In the “Type sequence” area, enter the three missing bases. To do this, type over the sample bases in the Type sequence row with the bases AAA. You may use small or capital letters but using capitals in this tutorial will allow you to see the changes more easily in the output file.
- Note the two sets of range boxes above and below the row where you just typed the missing bases.
- The upper range boxes need to show the sequence segment that occurs before the insertion point. In other words, “from the left end of the sequence until base 24.” In the left-hand box, ensure that one of the following is entered: 1, Left end, or lend (an abbreviation for “left end). In the right-hand box, type in the number 24.
- The lower range boxes need to show the sequence segment after the insertion point. In other words, “from 25 until the right end of the sequence.” In the lower pair of range boxes, type in 25 on the left. Acceptable choices for the right box are Right end or rend. If you knew the length of the sequence, you could also enter that number.
- The upper range boxes need to show the sequence segment that occurs before the insertion point. In other words, “from the left end of the sequence until base 24.” In the left-hand box, ensure that one of the following is entered: 1, Left end, or lend (an abbreviation for “left end). In the right-hand box, type in the number 24.
- To the right of the Save Results As button, type in pbr322-amended. This output file will automatically be saved in the working directory specified earlier.
- In the Format drop-down menu, choose the same format as the source file, Genbank.
- Save the finished SeqNinja script using the File > Save command. Navigate to the tutorial data folder (the path is provided in Step 3 of Part A: Setting up preferences). In the File name box, type Insertion.star. Then click Save.
The final script (below the comment) should now appear as follows:
Proceed to Part C: Running the script.
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