Sequence Submission Requirements – DNA Synthesis Program

When submitting sequences to the JGI DNA Synthesis program, please include the following items:

1. An Excel spreadsheet with two columns; one with the construct names, the other with the requested DNA or protein sequences. If you are providing protein sequences, we will also need to know what the destination host will be so we can select an appropriate codon table for the reverse-translation.
2. A list of restriction sites or sequences that must not be in the DNA synthesized
3. If you are providing any destination vectors, an annotated GenBank file of the sequence for each vector.
4. A GenBank file for each requested DNA sequence (see below), with the coding regions annotated. Other sequence features, such as promoters and terminators, can also be annotated.

DNA sequence files for all constructs should be emailed to Miranda Harmon-Smith, Synthetic Biology Project Manager.

Note: All input files for each program mentioned in this tutorial require plain text files in either FASTA or GenBank format. Files created using Microsoft Word will cause errors. To create a FASTA file in plain text use either TextEdit (MAC OS) or NotePad (Windows).

 

How To Create an Annotated GenBank File

There are several easy-to-use open source tools for converting FASTA files into well-formed GenBank files. Our prefered tool is VectorEditor, developed at the Joint BioEnergy Institute.

Alternatively, you can use ApE an open source desktop application written by M. Wayne Davis. This tool is better suited for very large sequences or ones that are very heavily annotated.

How to Use VectorEditor

Go to VectorEditor and follow the tutorial below to annotate your sequence and generate a GenBank file.

1. Go to File > Import File and select your file. Imported files can be FASTA or GenBank.
2. Click on the “.O” orange button in the top of the window to show Open Reading Frames.
   NOTE: You can also view your sequence’s Restriction Sites by clicking the “.C” blue button in the top of the window, and features like annotations by clicking the “.F” green button.
3. To make a sequence appear circular, click the button in the top left of the screen that looks like a multi-colored circle. For linear sequences, click the button directly to the right of the circular-sequence button.
4. Click on an Open Reading Frame to select its sequence, or hold the “COMMAND” button and drag your mouse over the sequence to select a specific region of the sequence.
5. Right-click the selected sequence, then click “Selected as New Feature”.
6. Enter your annotation information and click OK.
7. Go to File -> Download Genbank to download the annotated sequence.

How To Use ApE

To save your ApE file as a Genbank file, simply go to File -> Save As and add the characters “.gb” (no quotes, just .gb) to the end of your file name.