Highlighted methylation sites for restriction enzymes Quickly visualize restriction sites affected by Dam, Dcm and EcoKI methylation. Amino acid numbering Live numbering can now be shown alongside the translated amino acids on nucleotide sequences. Adjustable sequence selection Adjust either end of the selected region in the Sequence View by dragging. Batch edit annotations Quickly add or edit annotations in batch by copying properties from other annotations, sequences or documents.
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. 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. 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. 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. Import standard formats from public databases or external codon analysis tools. 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.
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, with new protein statistics added including charge at pH 7 and amino acid group counts. 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. Usability Tweaks to Increase Efficiency Enjoy an improved table of primers, drag and drop backbone selection for cloning, easier workflow management, better defaults, a less cluttered Sequence View and many other little tweaks and improvements. Patent Office requirements as well as other improvements.
Primer Characteristics 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. Silent Mutation Analysis for Restriction Sites Automatically identify point mutations in a coding sequence that will introduce a restriction site without affecting the protein.
Find sites in A and T rich sequences and with higher cleaving efficiency in vivo. No longer pull information from other sources. Now you can easily create your own enzyme sets. 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.
No more switching mirrors each time. If you set up a mirror in this way, Geneious can now connect to it natively. Includes automatic identification of compatible cut sites, and digestion and ligation with drag and drop ordering of fragments. Alignment Masking Mask unreliable alignment sites for better tree building, without deleting data. Manage alignment masking patterns using annotation tracks and automatically mask sites according to user defined criteria.
Improved Plasmid Viewer The new circular overview option helps you stay oriented by showing the bases of the sequence and the plasmid map alongside each other with synchronized editing, selection and scrolling.
Chimera Filtering Filter chimeric reads by comparing to a reference database, which can be any sequence list or alignment. For Windows, 64 bit Windows 10 with recent updates installed is required. This is a 10 bp region adjacent to the PAM site that can tolerate a maximum of 2 mismatches and 0 indels R Automate your cloning procedures or perform high-throughput batch cloning. For DNA sequencing, you can now discover structural variants and annotate them, allowing for correct alignments of read-ends around deletions and structural rearrangements in heterozygous samples.
Big Trees New search box for finding nodes and taxa, and automatic collapsing of sub-trees based on distances.
Greatly improved performance when loading and rendering trees. Options to control how many mismatches and indels are allowed when scoring against off-targets. VCF Export Easy exporting of single-sample variants.
Tadpole Brand new and super-fast de novo assembler with a very low miss-assembly rate. Most importantly, the sequence and alignment view is now scaled according to your display.
Sequence view Updated to new modern font for high quality publications, cleaner plasmid maps and retina screens. Assembly New workflow to run batch reference mapping of many data sets against many references, matching them up by name. Trees Sequences in the multiple alignment are now highlighted according to coloring in the tree. Lineage Parents and descendants are now shown with more information about the steps that have been performed and an HTML report can be exported with the full lineage.
Sequence Classifier Plugin Taxonomically classifies an organic sample by how similar its DNA is to your own database of known sequences using a BLAST-like algorithm with multiple loci and trees to assist with identification.
Greater Workflow Configurability New Genome finishing workflow and more options for creating custom workflows Easier Plugin Development Add your favourite algorithm, database or visualization to Geneious or write a plugin for your own new program and share it with the community New Plugins Extended functionality for tree building and viewing, alignment and assembly.
R8 Update 3 March, 8. Primer design and testing now have an option to match each sequence in an alignment instead of just the consensus Extract more annotation information Now you can select upstream, downstream and intergenic regions of matching annotations. Export Tree documents: Export to newick format may now include bootstrap support values New Plugins Blast2GO — All in one functional annotation tool and annotation data analysis.
FreeBayes — Haplotype-based variant detector for single sample analysis. 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.
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.
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 brings powerful analyses to increase accuracy and help transform collaboration. Highlights include updates to primer design, custom codon usage, import and export, annealed oligo cloning, restriction enzymes and shared database.
Custom Codon Usage Tables Back translate and optimize codons using your own codon usage tables. Import standard formats from public databases or external codon analysis tools. 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.
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, with new protein statistics added including charge at pH 7 and amino acid group counts.
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 GenBank format available for all individual sequences.
Sequence layout format to alter wrapping, numbering, sequence color and presence of reverse complement and translation. Primer Specificity 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.
Quick and easy primer pairing in the Sequence View to link two primers of your choice and calculate pair dimer Tm and product size. Restriction Enzymes Methylation sensitivity information shown in tool tip when mousing over a restriction enzyme. Sanger Sequencing Primer Design Quickly design primers for Sanger sequencing of vectors, inserts or other sequences. 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. Patent Office requirements as well as other improvements.
0コメント