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.

Plasmid and restriction mapping

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.

Molecular cloning with codon optimization tool

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.

Molecular cloning, restriction mapping and plasmid maps

Simulate molecular cloning operations in one-step

In a few clicks you can:

  • Ligate multiple fragments together that have matching overhangs
  • Insert a fragment of DNA into a vector with matching overhangs
  • Simulate restriction cloning
  • Simulate conventional PCR
  • Simulate InFusion Cloning and Gibson Assembly
  • Simulate TOPO cloning
  • Simulate Gateway and TOPO cloning
estriction analysis and molecular cloning with restriction enzymes

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.

Track molecular cloning operations

Automatically track and store important documentation

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


Gibson Assembly – Learn how to simulate Gibson Assembly in Geneious Prime.

TOPO Cloning – Learn how to simulate TOPO cloning in Geneious Prime, using TA, Blunt or Directional methods.

Restriction Cloning – This tutorial shows you how to use the restriction cloning tools in Geneious Prime to create a plasmid with a functional GFP fusion protein.

Golden Gate Cloning – Learn how to simulate Golden Gate cloning, including how to automatically design oligonucleotide primers for generating the overhangs for assembly of parts.

Application Notes

Homology-Based Cloning Methods – Design experiments using exonuclease-based recombination (3’ or 5’ exonuclease) or using homologous recombination.

More Geneious Prime Features

Primer Design – Design primers, find CRISPR sites, and optimize codons.

Assembly and Mapping  De novo assembly or reference mapping using industry leading algorithms, including TopHat and Velvet.

NGS Visualization and Analysis – Comprehensive analysis of data, including genome browser, contig visualization, SNP calling, and RNA-Seq expression analysis.

Alignment  Perform pairwise and multiple alignments of DNA or protein using trusted algorithms, including MAFFT and ClustalW.

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

Import Data – Import and convert common file types as well as their annotations and notes with a simple drag and drop

I have found Geneious to be one of the most intuitive and powerful sequence analysis programs that I have used in all my years working in the molecular biology field. Thanks for making my life so much easier.
Prof. John PayneUniversity of California