Geneious Prime 2021
Amino acid numbering (2021.1)
Live numbering can now be shown alongside the translated amino acids on nucleotide sequences.
New filter interface (2021.1)
Locate documents quickly in any table with the new filter button added to the status bar
Adjustable sequence selection (2021.1)
Adjust either end of the selected region in the Sequence View by dragging.
Geneious Prime gets a new look
Enjoy the new look and feel of Geneious Prime with an updated design, including new icons and font.
Highlighted methylation sites for restriction enzymes
Quickly visualize restriction sites affected by Dam, Dcm and EcoKI methylation.
Many other small improvements
- View the A correction factor on your protein and nucleotide translation statistics (2021.1)
- Improved workflow tools (2021.1)
- Accessible sequence viewer statistics
- Easily shareable documents
- Streamlined updating experience
- Improved Vector NTI / GenBank imports
- Added new genetic codes available on the NCBI list
- And more….
What Was Added in Previous Versions?
Geneious Prime 2020
|Longread sequence mapping with Minimap2 (external plugin)|
Fast and easy alignment of Oxford Nanopore and PacBio data to a reference sequence using an industry recommended tool, without the hassle of the command line
|Clustal Omega replaces ClustalW for better, faster alignments|
Scale up your alignments with Clustal Omega, now included with Geneious Prime. The HMM alignment engine improves both quality and speed of alignments compared to the older ClustalW aligner.
|Better back translate and codon optimization|
New codon optimization algorithm lets you match the codon usage from your organism of choice by generating a new sequence, starting from either a protein or nucleotide sequence. Optionally eliminate rare codons and restriction sites.
|More accurate annotation of CDS features onto your plasmids|
Automatic annotation of plasmids is now smarter with adjustment of CDS boundaries to match the nearest valid ORF when annotating single-interval CDSs from your reference features database.
|Add your favorite tools to Geneious with improved Wrapper Plugin system|
Can’t wait for us to add your favorite command line aligner, tree builder or assembler? You might be able to add it yourself from right inside Geneious using the Wrapper Plugin Creator plugin. Coding skills are not required, though a good understanding of command line interfaces and file formats is.
|Long Read de novo Assembly with Flye (external plugin)|
Fast de novo assembly of your raw Oxford Nanopore and PacBio long read sequences using Flye, suited to a wide range of applications including both single genome projects and metagenome assembly.
|Import Metadata on to Sequences and other Documents|
Seamlessly attach new data from downstream analyses or other applications onto your sequences in Geneious, or update document fields, by importing columns from a CSV/TSV format spreadsheet onto documents that are already in Geneious.
|Annotate from Database Improvements|
Easily identify and annotate the best matched features from a database on your plasmids and other sequences using the new extended database of standard plasmid features provided with Geneious, or use your own sequences as reference.
|Codon Optimization and Back Translation Improvements|
Customize the codon optimization parameters for your model organism by defining short sequence motifs to exclude from your optimized sequence, while easily generating multiple co-optimized versions of your sequence simultaneously.
|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.
|Wrapper Plugin System Improvements|
Customize Geneious with your own plugins using the wrapper plugin system, which now supports de novo assemblers, and running supported linux-only tools via the Windows Linux Subsystem.
|Analyze CRISPR Editing Results|
Easily align, cluster and visualize NGS reads from your CRISPR editing experiments. Analyze the frequency of variants and their protein effects from your application of choice, including HDR, NHEJ and base editors.
|Enhanced Search Options|
Quickly access your documents, folders, analysis tools and recently viewed items from a single unified interface.
|Codon Optimization Improvements|
Hover over your optimized codons for more information on synonymous codons and their frequencies.
Geneious Prime 2019
|Rapid Manual Primer Design|
Select desired binding site in the Sequence View to see real-time display of length and melting point (Tm) then easily add a primer annotation with a convenient new button.
|Powerful Primer Annotation Display|
5′ extensions (tails) on annotated primers are now displayed inside the sequence view to indicate the length of the extension, the nucleotides it contains and what functional elements are present such as restriction sites, spacers and tags.
|Simplified Testing and Annotation of Existing Primers|
Easily search all folders for primers that match a sequence of interest with the redesigned “Test with Saved Primers” operation. Copy and paste primers from other programs into the new “Add Primers” operation to find them on your target sequence in one step.
|Drag and Drop Sequence Export|
Export annotated sequences in GenBank format by simply dragging documents out of Geneious Prime and onto the desktop or into another program.
|Easy Extraction of PCR and Restriction Digest Products|
Shift click between two compatible primers or restriction enzymes for quick and easy extraction of their product from your sequence.
|Improved Protein Statistics|
Calculate on the fly statistics for protein sequences directly on nucleotide sequences within the Statistics panel
|Improved GenBank Export|
Export the information you need with your sequences using the simplified, flexible options to include your own Meta-Data fields and allow or constrain export parameters to suit downstream applications.
|Publish Plugins via Internal Network|
Create a curated list of plugins to offer privately to members of your organization via your internal network.
|Customizable Text View – Sequence Layout |
Format to alter wrapping, numbering, sequence color and presence of reverse complement and translation
|Customizable Text View – Alignment Layout|
Format to alter numbering, sequence color and highlighting of agreements/disagreements to consensus
|Customizable Text View – GenBank Format|
GenBank format available for all individual sequences
Primer specificity automatically tested within the template sequence when designing primers, and presence of any additional binding sites recorded on the primer annotation
|Primer Design Improvements|
Option to control the minimum distance between primers designed on the same strand – defaults to minimizing creation of duplicate primers when multiple primer pairs are designed together
|Annealed Oligo Cloning|
Added workflow to create a sequence with annotated overhangs representing the sticky ends created by annealing two partially overlapping oligos
|Sanger Sequencing Primer Design|
Quickly design primers for Sanger sequencing of vectors, inserts or other sequences
|Vector NTI Database Import|
Easily import your complete Vector NTI database with simple drag and drop, for both Vector NTI Express and Advance databases.
|Improved Text View Formatting of Sequences and Alignments|
Support formatting and export of sequences in accordance with U.S. Patent Office requirements as well as other improvements.
Quick and easy primer pairing in the Sequence View to link two primers of your choice and calculate pair dimer Tm and product size.
|Easier Shared Database Rollout|
Immediately access shared data and get straight to doing your research with a Geneious Shared database connections now able to be pre-configured by your IT team or admin when rolling out a version of Geneious Prime. Includes improved support for Windows authentication.
|Volcano Plots for RNA-Seq Expression Analysis|
Visualize gene expression in an interactive volcano plot that can be used to highlight and jump to differentially expressed genes.
|Pretty PCA Plots|
Create beautiful PCA plots with better labelling and new visualization options.
|Silent Mutation Analysis for Restriction Sites|
Automatically identify point mutations in a coding sequence that will introduce a restriction site without affecting the protein.
|CRISPR Cpf1 Option|
Added support for CRISPR-Cpf1 with a 5’ PAM site. Find sites in A and T rich sequences and with higher cleaving efficiency in vivo.
|Create Enzyme Sets|
What’s in the freezer? No longer pull information from other sources. Now you can easily create your own enzyme sets.
|Better FASTQ Import|
Paired reads can be associated with each other during import and Geneious will do it’s best to guess how they’re paired. Read technology can also be set.
|Updated Mauve Plugin for Bacterial Genome Alignment|
Now includes support for sequence lists and the MCM operation for reordering contigs, making it possible to align draft genomes and perform genome finishing.
|CRISPR-Cpf1 Specificity Scoring|
Confidently pick the best CRISPR-cpf1 guide RNA sites using a new specificity score which is calculated from an off-target analysis against your database of choice.
|Smart NGS Import |
Drop any assortment of SAM, BAM, GFF, BED, and VCF files into Geneious to import in one easy step, even if you have a mixture of different samples and reference sequences.
|Better BLAST Server Management|
Set up several BLAST server mirrors at once and choose the best one each time you do a search. No more switching mirrors each time.
|NCBI BLAST Cloud Support|
It’s never been easier to set up your own BLAST mirror thanks to NCBI BLAST Cloud. If you set up a mirror in this way, Geneious can now connect to it natively.
|Concatenate by Index|
Concatenate sequence lists and alignments by index, rather than by name, which is super useful for merging paired reads that don’t quite overlap.
|CSV/TSV Export of Sequence Lists|
Export all of the sequences in a sequence list along with their metadata to CSV or TSV so you can drop them in Excel or similar for further analysis.