Geneious Prime
Description
Geneious Prime is a graphical user interface (GUI) based bioinformatics package that contains a suite of tools for molecular biology and Next Generation Sequencing analysis.
Listing of Analysis Functions
Classic Computational Molecular Biology Tools
- View/edit nucleotide or amino acid sequences
- Obtain complement and reverse complement of nucleotide sequences
- Convert between DNA and RNA
- Translate nucleotide to amino acide sequences
- View, edit, extract, and compare sequence annotations
- Examine sequence chromatograms
- Run simulated nucleic acid gels
- Viewer for
- Interrogating RNA or DNA secondary fold structure
- Examining protein 3D structure
- Perform sequence alignment using the following algorithms
- BLAST
- Geneious algorithm
- MUSCLE
- ClustalW
- MAFFT
- Construct phylogenetic tree
- PCR primer design
- Identify primer characteristics
- Predict PCR products
- Molecular cloning
- Identify CRISPR sites and analyze editing results
- Perform microsatellite analysis
- Microsatellite analysis
NGS tasks
- Reference based read mapping
- De novo assembly
- Trim reads using BBDuk
DNA sequencing
- Variant calling
Gene expression
- Calculate expression counts
- RNA sequencing - the algorithms below are available to find differentially expressed genes.
- Geneious Prime built-in method
- DESeq2
Microbial
- Metagenomics
Visualizations
- Genome browser
Information mining
- Databases from the National Center for Biotechnology Information (NCBI) including:
- Gene
- Genome
- Nucleotide
- Popset
- Protein
- Structure
- Taxonomy
- PubMed
- UniProt
Recommendations
- Geneious Prime can not be used for epigenetic analysis. Please see Partek Flow or CLC Genomics Workbench for this functionality.
- This package does not support pathway or gene ontology analyses. Please see Partek Flow, Partek Genomics Suite, Qiagen Ingenuity Pathway Analysis (IPA), or Qlucore Omics Explorer to gain insight on the network and pathway level.
- Single cell RNA sequencing analysis cannot be performed using Geneious Prime. Use Partek Flow or Qlucore Omics Explorer.
Things to Know
Geneious Prime runs on a user's local machine and may be limited by the available compute resources on that machine.
Input Data Types
- CSV
- TSV
- TXT
- FASTA
- FASTQ
- SAM
- BAM
- VCF
- BED
- GFF
- GTF
See the Geneious Prime User Manual for a full list of supported input file types.
Output Data Types
- TXT
- CSV
- TSV
- VCF
- FASTA
- FASTQ
- GFF
- BED
- SVG
- EMF
- PNG
- JPG
See the Geneious Prime User Manual for a full list of supported export formats including formats for exported images.
Access Information
You must submit a request through service.cancer.gov to obtain access to this package. This software requires access to a floating license server, and so care should be taken to return licenses when the software is not actively being used (i.e. close the application). OSTR holds 10 concurrent licenses of Geneious Prime. You need to either be on the NIH network or VPN to use this package.
Getting Help
- A help menu is built into the Geneious Prime user interface.
- The Geneious Prime User Manual is also available to users.
- There are also tutorials that guide users through various Geneious Prime analysis workflows.