Primer design and testing

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

Built in primer database and browser

Drag and drop your primers in FASTA, spreadsheet or Genbank format. Once loaded, you’ll have them all as primers in your own searchable database. Geneious Prime will let you know if you already have primers that match a new sequence.

Elegant primer design tool

Design PCR and sequencing primers and hybridization probes, to any target region or entire sequence, directly on alignments and assemblies in the Geneious sequence viewer. Add and remove extensions to a primer sequence before, during or after the design process.

Primer specificity testing

Be confident your primers will only bind in a single location with automatic identification of any additional, off target, binding sites found when using Test with Saved Primers. Off-target information for the tested document will be added to the new primer annotations.

Test PCR primers against any sequence before your order

Geneious Prime is packed full of features to help you get the most from your PCR experiments.

  • Screen for physical properties, hairpins and primer-dimers
  • Select all PCR products on a sequence or any two primers in a pair to extract the product of those primers
  • 5′ primer extension – Extend a primer with a restriction site, polyA tail or any other custom sequence
  • Dynamically calculate the DNA melting point for a selected region for manual primer design
Tutorials

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

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

More Geneious Prime Features

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.

Molecular Cloning – View plasmid maps, automatically annotate vectors, find restriction sites; digest, ligate, and perform Golden Gate, Gibson, and Gateway cloning.

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

Geneious is far less expensive than some other software and I would NEVER consider switching given Geneious’ power and ease of use.
Prof. F. Paul DoerderCleveland State University