Genome annotation, sequence analysis and variant calling

Automatic genome annotation, real-time sequence analysis and protein structure prediction. Powerful SNP detection and variant calling.

Discovery is easy with automatic genome annotations

Automatically annotate a new genome based on existing patterns and annotations in public or local databases including annotating ORFs as hypothetical genes based on these patterns and queries against NCBI.

  • Annotate sequences with ORFs or predict genes with Glimmer
  • Search for motifs by copying and pasting sequences
  • Similarity based annotations (large database of sequences)
  • Transfer annotations using an alignment
  • Detect tandem repeats with Phobos

Powerful SNP detection and variant calling

Navigate reads in a beautiful browser. Easily identify, examine and resolve disagreements manually in the sequence viewer or quickly annotate variations on larger contigs. This feature can be configured to

  • Screen read errors by finding disagreements above a minimum threshold.
  • Find disagreements only in coding regions
  • Identify the effect of variations on protein translations, including those where only the first and third positions in a codon vary
  • Calculate the probability of a SNP being correct
  • Eliminate SNPs with a high strand bias
  • Export your variants to csv
  • Search and annotate short structural variations such short tandem repeats (STRs) and insertion and deletion events (InDels)

Real-time sequence prediction

In a few clicks you can find so much about your sequences including;

  • DNA translation – Translate and complement alongside your nucleotide sequences. Translate in any frame or all 6 frames at once or just translate the annotation or selection that you’re interested in.
  • Consensus Sequence – Predict consensus sequences according to your choice of identity schemes including “consensus by quality” on chromatogram data which chooses the best base call automatically
  • DNA sequences – Predict identity, read coverage, numerous statistics on base frequencies, residue frequencies, CpG islands and more
  • Protein sequences – Predict molecular weight, isoelectric point, hydrophobicity, transmembrane regions, coiled coil regions, amino acid charge and more

Automatic Annotation in Geneious


Pairwise Alignment – Develop the skills needed to align pairs of DNA and protein sequences with Geneious using dotplots and alignment algorithms.

3D Structures – Explore the controls in the Geneious 3D structure viewer and learn how to use it to visualize active sites in a protein structure.

Application Notes

Creating SNP Trees – An overview of how to generate a SNPtree using next generation sequencing data from Ebola virus isolates.

More Geneious Prime Features

Assembly and MappingDe 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.

AlignmentPerform 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.

Import Data – Import and convert common file types as well as their annotations and notes with a simple drag and drop

I have found Geneious to be one of the most intuitive and powerful sequence analysis programs that I have used in all my years working in the molecular biology field. Thanks for making my life so much easier.
Prof. John PayneUniversity of California