Mar 09, 2023
Submitting Genomes
- 1UCSF
Protocol Citation: emma.pearce 2023. Submitting Genomes. protocols.io https://dx.doi.org/10.17504/protocols.io.8epv5jdkdl1b/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: In development
We are still developing and optimizing this protocol
Created: February 14, 2023
Last Modified: March 09, 2023
Protocol Integer ID: 77005
Keywords: bankit, submitting, ncbi
Abstract
Steps to submit a genome to NCBI through Bankit
Submitting to Bankit
Submitting to Bankit
Log into Bankit with UCSF username and password:
- Follow this link: https://www.ncbi.nlm.nih.gov/WebSub/?form=history&tool=genbank
- Choose more login options and select University of California, San Francisco
Select "Start Bankit Submission"
Fill out the contact information
Sequence Authors:
List all sequence authors (use the Add button for more than one)
Reference Information #1:
Select publication status (unpublished, in-press, or Published)
- If in-press add reference title, journal title, year, volume, issue, and page numbers
- If published add reference title, journal title, year, volume, issue, page numbers, and PubMed ID
- Optional: if unpublished add reference title
Select reference authors as "Same as Sequence Authors" or "Specify New Authors"
- If specify new authors, list authors
(Optional) Add Another Reference:
Follow Reference Information #1 steps
Sequencing Technology:
Select the sequencing technology (or other and specify)
Select unassembled sequence reads or assembled sequences (consisting of two or more sequence reads)
List assembly program and version or date
Example: Illumina, Geneious v. Geneious Prime 2023.0.1
Submission Release Date:
Select "Immediately after processing" or "Release date"
- If Release Date is selected, specify date in DD-Mon-YYYY format
Sequence(s) and Definition Line(s):
Choose molecule type, linear or circular, if it is a complete sequence, and fasta or alignment format
Either download sequence file or copy and paste it in the box
- Note: make sure the first line follows this format; make everything in bold specific to your submission
>Seq#[organism=genus species] species straininfo
Example: >Seq1[organism=Enterovirus rhinovirus] Rhinovirus C17 strain RvC17/USA/2019
Submission Category:
Select "Original" or "Third Party Annotation"
Source Modifiers:
Choose organelle/location if applicable
Choose source modifiers and list information in value column, add as many as desired
Example: Strain = RvC17/USA/2019, host = homo sapiens, tissue_type = Lung, country = USA, collection_date = 2019
Features (Overview):
Select "Add features by completing input forms"
Select "Coding Region (CDS) / Gene / mRNA"
Select "providing intervals"
Click Add
Features (Detail):
Choose if the CDS is on the + or - strand
If the CDS is not compete, select 5' or 3' for which end it is incomplete at
Select "Entire Sequence" or "Specific Spans" for Nucleotide Interval Spans
- If Specific Spans, specify start and stop and which strand it is on
List protein name (optional: also list protein description and EC number)
Click accept
Example: specific spans: start = 19 stop = 6498 strand = -minus; protein name = polyprotein
Review Submission:
Make sure everything looks good
If resubmitting check the box under the resubmission section