Select the alignment and select Tools→Submit to GenBank. Give your submission a name (e.g. Tutorial 2) and ensure "Save a local file" is checked as we do not want to submit the sequences from this tutorial to GenBank. Keep the same Publisher Details as for Exercise 1, with your name and address details entered and "TEST" entered as the Reference Title.
This alignment represents a population study, as it comprises sequences of the same mtDNA region isolated from 6 different individuals of the same species. We can indicate this by choosing Population Study under Submission Type.
Enter a project name, such as "tuatara mtDNA", then map your document fields to GenBank fields as follows:
*Note that Collection Date must be a recognised date field, and only these fields will show up in the drop-down options.
We also wish to add Isolation source and Isolate name as fields, so that information on the sampling location and sample name is given along with the sequence.
Map these fields by checking Include extra fields then clicking Choose. Add the fields Isolation Source and map it to Description, and Isolate, mapped to Name. Note that Sequence ID is also mapped to "Name", however the Sequence ID is only used for identifying the sequence through the submission process, so for the ID to appear in the GenBank flat file it should be mapped to another field.
To add the sequence annotations into our submission, check the Include Features/Annotations box. Make sure Add Gene & CDS features using fields is unchecked, as these sequences do not have protein-coding genes. Include quality scores, Include structured comments and Include Primers should also be unchecked.
Your Submit to GenBank dialog box should now look like this:
You can now click OK to test the submission, but before you do this double-check that you have chosen to Save as a local file, not Upload submission, as we do not want to submit the tutorial sequence to GenBank! After you click OK, you will get a discrepancy report. This is given for every submission and does not necessarily mean your submission contains errors. If there are errors that are likely to interfere with the submission you will see a Validation Errors/Warnings window instead, detailing errors that should be attended to before the submission proceeds.
If you wish to see a preview of what your submission will look like in Genbank format, click the Genbank Preview tab above the Discrepancy report.
Click Continue and save the .tar file to your desktop. You have now completed a test submission of a mitochondrial DNA alignment. If you wish to submit real data to GenBank, simply check the Upload submission box rather than Save a local file.
Congratulations, you have now completed the GenBank Submission Tutorial. For troubleshooting click here.