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.

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.

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

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.

Automatic Annotation in Geneious Prime


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

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.

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

Primer Design – Learn how to import, design and test oligonucleotide primers, primer-pairs and primer-pair/probe combinations

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 and optimize codons.

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

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

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