Getting Started with Geneious Prime

Learning how to use Geneious Prime is easy! We developed a few short videos to help guide you through the process. From how to import your data to aligning your first sequences, follow these tutorials and you will master the basics in no time.

Course Content

Import and Organize Your Files
Introduction to Sanger Sequencing
Perform Analyses
Perform Restriction Cloning

View Documents and Sequences
How to Design Primers
Find and Analyze Restriction Enzymes
Annotate Sequences

Import and Organize Your Files

Learn how to import new files and sequences, organize the folder system, and search for documents.

LENGTH 5 minutes

View Documents and Sequences

Overview of the sequence viewing options, including how to zoom, annotate, split the view and change the colors of your sequences.

LENGTH 6 minutes

Introduction to Sanger Sequencing

Learn how to check sequence quality, trim the ends and map chromatogram sequences against a reference. Then view the contig and edit bases.

LENGTH 5 minutes

How to Design Primers

Automatically design new primers, adjust melting temperature, length, hairpin and GC content, and extract PCR product from a primer pair.

LENGTH 6 minutes

Perform Analyses

Run analyses such as BLAST, alignment, primer design and cloning, choose your method or algorithm, adjust settings and find more information.

LENGTH 2 minutes

Find and Analyze Restriction Enzymes

Select enzymes to simulate an agarose gel, view and export fragment information, and create a custom enzyme set.

LENGTH 5 minutes

Perform Restriction Cloning

Select a vector and insert for restriction cloning, choose enzymes, add additional inserts or rearrange inserts, and view the final cloning product.

LENGTH 3 minutes

Annotate Sequences

Display annotations on your sequence or in a table. Learn to import, transfer, and automatically add annotations to your 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.