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Geneious Prime

Description

Geneious Prime (Dotmatics) is a user friendly graphical user interface (GUI) based bioinformatics package that contains a suite of tools for molecular biology and sequencing analysis. Geneious Prime is capable of handling data from several types of high throughput sequencing experiments, including RNA sequencing. See below for a list of analysis functions.

Listing of Analysis Functions

Classic Computational Molecular Biology Tools

  • Sequence alignment using the following algorithms
  • BLAST
  • Geneious algorithm
  • MUSCLE
  • ClustalW
  • MAFFT
  • Construct phylogenetic tree
  • PCR primer design
  • Identify primer characteristics
  • Predict PCR products
  • Cloning
  • In silico digestion and ligation
  • Identify CRISPR sites
  • CRISPR editing analysis
  • Sequence classification
  • Visualize protein 3D structure
  • Convert between DNA and RNA
  • Microsatellite analysis

NGS tasks

  • Reference based read mapping
  • De novo assembly

DNA sequencing

  • Variant calling
  • DNA forensics analysis

Gene expression

  • 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 does not include a workflow to conduct 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.
  • There is no workflow for single cell RNA sequencing. For this, refer to 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.

Additional file types accessible to Genious Prime include DNAStar (SEQ, PRO) files. Note that Geneious Prime and SnapGene are developed by the same company, Dotmatics.

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
  • PDF
  • VCF
  • FASTA
  • FASTQ
  • GFF
  • BED
  • PDF
  • 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.