Molecular Cloning

Automatically annotate plasmid maps and expression vectors. Simulate a variety of molecular cloning operations including restriction cloning, Gibson Assembly, Gateway cloning and TOPO cloning.

Simulate molecular cloning operations
  • Ligate multiple fragments together that have matching overhangs
  • Insert a fragment of DNA into a vector with matching overhangs
  • Simulate:
    • Restriction cloning and PCR
    • Golden Gate cloning
    • In-Fusion Cloning and Gibson Assembly
    • Gateway and TOPO cloning
    • Parts cloning
Automatically annotate plasmid maps and expression vectors

Geneious Prime is connected to PlasMapper which allows you to automatically highlight plasmids with common promoters, terminators, cloning sites, restriction sites, reporter genes, affinity tags, selectable marker genes, replication origins and open reading frames.

Codon Optimization Tool

Find rare codons or produce a fully optimized sequence based on a target organism and remove unwanted restriction sites at the same time.

Store and access important restriction enzyme and DNA fragment data

Drag and drop your important data, customize your restriction enzymes lists and display all of the enzymes on your linear or circular DNA fragment-all in real time. Commercially available enzymes including GoldenGate and BioBrick are already stored in Geneious Prime.

Automatically track and store important documentation

Track cloning operations so changes can be propagated automatically from parents to all descendants.




Cloning, CRISPR and Primer Design

Learn how to design primers, simulate cloning and find and analyze CRISPR sites with videos and tutorials.

BLAST, GenBank and Automation

Learn how to set up automated workflows, BLAST search and connect to GenBank.

Tutorial: Transferring Annotations

Learn how to quickly annotate a sequence by transferring annotations from related sequences.

Tutorial: Gateway Cloning

Learn how to simulate Gateway cloning, including designing attB-linked oligonucleotide primers, BP and LR reactions, and Multisite.



Find CRISPR sites, design guide RNAs and analyze your editing results

Primer Design

PCR and sequencing primer design tool. Primer database and testing.

Sanger Sequencing

Trim, assemble, and view Sanger sequencing trace files. Powerful SNP detection and variant calling.


Connect to NCBI and PubMed, submit sequences directly to GenBank, BLAST sequences and search your own database.

Geneious has done a great deal for our lab, and I think it adds incredible value for labs with a mixture of wet and dry folks or those doing lots of cloning like ours.  
Cole TrapnellHarvard University