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

Introduction to Sanger Sequencing


Assembling Chromatograms – Learn how to edit and assemble chromatograms from raw sequencing data for downstream analyses.

Transferring Annotations – Learn how to quickly annotate a sequence by transferring annotations from related sequences.

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.

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