Getting Started with Geneious Prime

The Getting Started video series teaches new Geneious Prime users eight core workflows: importing and organizing sequence files, viewing and annotating sequences, Sanger sequencing analysis, automated primer design, BLAST and alignment searches, restriction enzyme analysis, and restriction cloning. Each video runs 2 to 6 minutes and uses real sequence data to demonstrate workflows end to end.

Course Content

Import and Organize Your Files

Import FASTA, GenBank, and BAM files into Geneious Prime by drag-and-drop, or search NCBI's Nucleotide, Protein, and PubMed databases directly. Organize files in color-coded folders and find them instantly with the real-time search bar.
LENGTH 5 minutes

View Documents and Sequences

View files in the Geneious Prime document viewer, using tabs for Text View, Lineage, and sequence data. Zoom, split the view, recolor bases, and toggle annotations, translations, and GC content graphs from the control panel.
LENGTH 6 minutes

Introduction to Sanger Sequencing

Trim poor-quality bases from chromatogram sequences, then map them to a reference with Align/Assemble > Map to Reference. Review the contig, edit bases, and save changes to the chromatograms or contig only.
LENGTH 5 minutes

How to Design Primers

Automatically design PCR primer pairs by setting product size, melting temperature, and hairpin or dimer penalties, or create primers manually. Extract the PCR product, design sequencing primers, and export details as a table.
LENGTH 6 minutes

Perform Analyses

Run analyses in Geneious Prime via toolbar shortcuts to BLAST, alignment, tree building, primer design, and cloning, each with its own settings. This video demonstrates a pairwise alignment and highlights the built-in help buttons.
LENGTH 2 minutes

Find and Analyze Restriction Enzymes

Find restriction sites using built-in or custom enzyme sets, filtering by cut frequency and region. Review results in the Enzymes and Fragments tables, simulate an agarose gel, export fragment data as CSV or TSV, and build custom enzyme sets.
LENGTH 5 minutes

Perform Restriction Cloning

Simulate restriction cloning by selecting a vector backbone and PCR product insert, then choosing enzymes from sequence annotations or a custom set. Add multiple inserts, run the simulation, and view the final concatenated sequence.
LENGTH 3 minutes

Annotate Sequences

Add annotations by importing GenBank, BED, or GFF files, or creating them manually. Detect annotations automatically using Live Annotate & Predict against reference files, or transfer annotations between aligned sequences.
LENGTH 6 minutes

Common Questions About Geneious Prime

What does the Getting Started video series cover?

The Getting Started series is eight short videos covering the core workflows new users need: importing and organizing files, viewing sequences, Sanger sequencing basics, primer design, BLAST and alignment analyses, restriction enzyme analysis, restriction cloning, and sequence annotation.

How do I design primers in Geneious Prime?

The automated primer design tool targets any region on a sequence, with adjustable parameters for melting temperature, length, GC content, and hairpin formation. It screens for primer-dimers and off-target binding sites, and supports both basic and degenerate primer design.

How do I import sequence files into Geneious Prime?

Geneious Prime supports drag-and-drop import of formats including FASTQ, GenBank, FASTA, SnapGene (.dna), Excel, SAM, BAM, GFF, BED, and VCF. You can also import directly from NCBI databases within the software.

What Sanger sequencing analysis can I do in Geneious Prime?

Geneious Prime handles end-to-end Sanger analysis: import ABI trace files, check quality, trim ends, and assemble chromatograms against a reference to produce an editable contig with variant inspection.

How does restriction cloning work in Geneious Prime?

Select a vector and inserts, choose compatible restriction enzymes, arrange the fragments, and preview the final construct. Geneious Prime simulates the ligation product and tracks parent-to-descendant lineage across cloning operations.

Where can I find more learning resources after the Getting Started series?

Geneious Academy covers NGS mapping, phylogenetics, BLAST, and advanced cloning through additional video series, tutorials, and guides. The User Manual provides full reference documentation, and the Help Center has a searchable knowledge base for installation and licensing questions.

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