The Genbank Submission plugin allows you to submit your contigs to Genbank once you have completed all edits. You will need the following to get started:
- A Bankit and NCBI FTP account (contact NCBI to obtain one)
- The Genbank Submission plugin (available from the main page of this wiki)
Preparing your submission
If you did not install the genbank submission plugin when you set up the biocode plugin, do so now. Once the plugin is installed, select the contigs and/or sequences that you want to submit to genbank, and click Tools > Submit to Genbank. You should then fill in the options and fields according to the following guidelines:
- The submission name is a free form field, and will not actually affect the results of your submission. Enter whatever you like here.
- Click Edit Publisher Details... to edit your author/publication information. This information is preserved between submissions, so you should not have to change most of it, but it is still good practice to double check it before each submission.
The next set of options matches fields annotated to your documents. You may choose a field from the dropdown to map a field on your documents to a genbank submission field. The required fields are displayed in the main dialog. If you want to add optional fields, click the Additional Source Fields... button. You can choose the fields you want from the dropdown, and click the + button to add more fields.
If the Include Features/Annotations checkbox is checked, the plugin will include any sequence annotations on the consensus sequences. If your annotations match the standard NCBI annotation types (and qualifiers) they will be copied directly. Other annotation types and qualifiers will be converted to misc features. See http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html#7.2 for a list of valid types and qualifiers.
Consensus, Primers, and Traces
The tabs at the bottom of the dialog represent extra data that you can attach to your submission.
- Consensus: If you have selected contigs, you can choose the options for building the consensus (which is what is finally submitted to genbank as your sequence).
- Traces: If you have selected documents with traces, the traces tab will be displayed. The required fields are variable, so the options you see will change depending on what values are selected. Again, you can use the additional fields button to add optional fields to your submission.
- Primers: If you are submitting sequences annotated from the LIMS, then primers will have been annotated on your sequences as document notes. If not, you can annotate the primers yourself by clicking the notes tab when viewing the selected documents, and choosing Sequencing Primer in the Add Custom Note dropdown. Choose the document fields that correspond to your primers' names and sequences.
Validation and submission
You have a choice of either generating a submission file, or uploading the submission directly to NCBI (you will need a BankIT and FTP account to do this). You can make your choice at the top of the submission options dialog. If you are updating an existing submission, you can choose the update option, and enter the BankIt id in the field provided. Otherwise, choose Upload New Submission, and a new submission will be created for you.
Your submission will be validated using tbl2asn, and you will be shown any problems before the submission is commenced. The validation result window has two tabs.
- The Validation errors/warnings tab shows you a list of errors that may prevent your submission from being accepted
- the Discrepencies tab shows you potential errors that you may have made, based on common errors made in genbank submissions.
It is recommended that you thoroughly review the information in both tabs before proceeding.
If you have chosen to automatically upload your submission, further validation will take place on the server once the upload is complete. Geneious will inform you whether your submission has been Accepted, Accepted with Warnings, or Rejected. You should also recieve an email from Genbank detailing your submission. Once your submitted sequence(s) have been assigned accession numbers, you should recieve a further email from genbank with the details.