Working with GenBank in Geneious Prime

This GenBank series shows how to search NCBI’s nucleotide, genome, and PubMed databases from Geneious Prime, downloading sequences, genomes, and citation-ready references. Two more videos cover preparing a sequence for submission, adding required gene, CDS, and exon qualifiers, then submitting it through the GenBank Submission plugin with a discrepancy report. Three videos.

Course Content

Accessing GenBank

Search NCBI’s Genome, Nucleotide, and PubMed databases from the Sources panel in Geneious Prime, downloading full sequences, annotated genomes, and citations. Export references as EndNote or BibTeX, and drag results into a local folder before they clear.
LENGTH 4 minutes

Prepare for GenBank Submission

Prepare a small sequence (mRNA, organelle, plasmid, or small genome) for GenBank by entering general metadata, then add required gene, CDS, and exon qualifiers, including translation table, codon_start, and partial-feature flags where relevant.
LENGTH 6 minutes

Submit to GenBank

Install the GenBank Submission plugin, then submit a prepared sequence via Tools > Submit to GenBank, adding publisher details and mapping metadata fields. Resolve any validation errors in the discrepancy report, then save a tar file or upload it.
LENGTH 6 minutes

Recommended Resources

What can I submit with the Genbank Submission plugin?

A list of what you can and can’t submit using the GenBank plugin.

Genbank Submission common errors

Troubleshooting GenBank submission errors.

Geneious vs GenBank

Nomenclature and exporting of Geneious Prime files in GenBank format.

More Geneious Academy

TUTORIALHow to Access GenBank from Geneious Prime
Search GenBank from inside Geneious, download nucleotide sequences, taxonomy and publications, and run BLAST.
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TUTORIALHow to Submit to GenBank from Geneious Prime
Format sequences and alignments for GenBank, add the required metadata, and correct annotation qualifiers.
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VIDEO SERIESSearching with BLAST in Geneious Prime
Search with BLAST in Geneious Prime, single or in batch, against GenBank or a custom database, then review hits by E value, identity, and length.
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VIDEO SERIESCreate Automated Workflows in Geneious Prime
Build a custom workflow in Geneious Prime from Sanger trimming to tree building, then scale it across document sets using parallel steps and branching.
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