Sequences represent any piece of DNA, whether it is a plasmid you have in the fridge or a construct you intend to produce with an assembly. You can create a new sequence from scratch or upload them in bulk.
To open the DNA Sequences library, click Molecules > DNA Sequences in the top explorer menu. Here you can find a repository of DNA sequences that you have created or uploaded.
To create a new sequence you click on the "New Sequence" button which gives you the option to start with a completely empty sequence. This will pop up a "Create New Sequence" window where you will be asked to enter a sequence name and description, select the checkbox if you want it to be circular and click Save. You will be taken to the Vector Editor tab where you can start creating your sequence.
To import sequences, click the "Upload Sequences" button. This opens the Upload Sequences dialog. Browse for sequences on your computer to import them. You can select and open or simply drag and drop a folder or file to the dashed area of the window.
Currently, our Design Module supports the following file formats: .gb, .gbk, .csv, .fasta, and .zip. You can find the template for .csv file by clicking the "Download Example CSV File" at the bottom of the dialog.
You also have the following actions to perform when uploading your sequences:
1. Library: Set a library field on your sequences so you can easily search and sort them. All sequences imported will be associated with this library which allows you to group them accordingly.
2. Use file name as sequence name: For files that contain a single sequence, use the file name as the sequence name.
3. Auto Annotate Features: Automatically create features that match on base pairs with a list of existing features that you select.
4. Auto Annotate Parts: Automatically create parts that match on base pairs with a list of existing parts that you select.
5. Create Features from Sequences?: Create features on these sequences that span the entire sequence and take on the name of the sequence. If this box is checked you can also choose a type for the features created.
6. Create Parts from Sequences?: Create parts on these sequences that span the entire sequence and take on the name of the sequence. If this box is checked it gives you the option to apply tags to the parts created. Select these tags from the dropdown menu. You also have the option to offset the start and end of those parts (+/- X amount of bps).
Note that when importing a GenBank file, you might see a warning in case the file contains annotations that do not have a 'label' attribute. If this is the case, when the sequence is rendered, there will be some features that will not have a name. Also, you may see a warning if two or more sequences have the same GenBank locus name or sequence content. These duplicates can still be imported but this check helps prevent duplicated content in your library.
Once the import is completed these sequences will appear in your library.