NovoBuilder is a free, online tool for molecular biology that integrates plasmid sequence annotation, plasmid design, codon optimization, and automatic quote.
1. Backbone vector selection: Click on the icon on the left side of the panel, there will be a search box, a list of host cell type list, and a text box.
a) From the list we can select vectors for specific purposes. For example, if we click “Bacteria”->” Cloning”, we will find the pUC57 vector for plasmid cloning. Double-click the pUC57 vector we will see a pop-up box, here we can enter the plasmid construct name, click the “OK” button and a plasmid map will appear in the middle of the page (map panel), on the right side (sequence panel) displays information such as plasmid sequence and restriction enzyme sites.
b) Alternatively, we can also search the vector name. For example, if we input “PUC” in the search box, it will return vectors containing “PUC”, like pUC57-Kan, pUC57, pUC18 and etc. Double click pUC57 vector we will see a pop-up box, enter the name of the plasmid construct, and then click the “OK” button. There will be a plasmid map in the center of the page, and on the right side of the page displays the plasmid sequence, restriction enzyme sites, and other key information.
c) Paste your own plasmid sequence in the text box, then click the “UPLOAD SEQUENCE” button, in seconds, NovoBuilder will return the annotated map and sequence.
2. Prepare the target sequence:
In most cases, the main purpose is to insert the designed DNA, we only need to copy the target sequence. If the inserted target sequence is a common component, such as the EGFP gene, or U6 promoter, you only need to click on the icon. Then there will be a search box and a list of component types on the left sidebar. Entering the name of the component in the search box will return our collection of commonly used components. Double-click on a specified component and an information box will pop up. It displays information about the component's name, type, function, and most importantly, sequence. Then we can click the corresponding button in the pop-up window to copy the protein/DNA sequence of the component.
3. Insert/modify sequence: In the right sequence panel, we can single-click or drag the mouse to select a sequence. Then right-click to select Insert from the pop-up menu or use the keyboard CTRL+V, and it will pop up an insert/replace window. This window allows you to customize the inserted fragment, including its name, type, orientation on the map, and DNA sequence. If no DNA sequence is selected in the right sequence panel, there is only insertion and no replacement. The selected DNA sequence will be replaced by the newly copied sequence, so we can Insert/modify the target sequence.
4. Delete sequence: drag the mouse in the right sequence panel to select the target DNA sequence. Then click the right mouse button, and select Delete from the menu or press the Del or Backspace on the keyboard, a confirmation box will pop up, click OK to save the deleted sequence.
5. Edit Features: Right-click the marker of the feature to be edited from the right sequence panel or the middle mapping panel, and select Edit Feature from the pop-up menu. An Edit Feature window will show, where you can modify the name, type, direction of the marker, start and end positions, color, etc. of the feature. and so on.
6. Codon optimization: Select a coding region sequence (>=18 bp and a multiple of 3 bp) from the right sequence panel. Then click the right mouse button, select Optimize Codon from the pop-up menu, and set the parameters for codon optimization.
7. Save construct design: Right-click in the map panel and select Archive Map to save the current design. Even if you close the browser, you can still see the archived plasmid design on the tool's home page the next time you open it. By default, the plasmid will be saved permanently unless you clear the browser cache.
8. Export Map: Right click in the map panel and select Export Map(.gb) from the pop-up menu to export the plasmid map to Genbank(.gb) format.
9. Ordering: Right-click on the plot panel or sequence panel, and select “Ordering”. Then a quote window will pop up. If the backbone vector was uploaded by you, such a quote window will not pop up, please contact us for a quote. If the target sequence contains multiple repeats, local very high/low GC content, and other particularly difficult sequences, the pop-up window will not show the price, please send us an email for a quote.
10. Others: During plasmid design, NovoBuilder will automatically save the plasmid profiles every 5 minutes, and the default time of auto-save is 7 days. More features can be explored by clicking the right mouse button.
11. Bug report: If you find any bugs or have any suggestions, please do not hesitate to send an email to： email@example.com