Predict, Manipulate and Annotate in Geneious Pro™

Geneious Pro™ includes numerous useful features for manipulating sequence data, displaying real-time prediction graphs, analyses and annotations, and the ability to predict and annotate permanent annotations.

Useful tools for Sequence Manipulation

• Manual editing – Edit your sequences intuitively. Over-write, insert, drag, extend and more
• Extract annotations – Batch extract annotated regions matching your criteria from multiple sequences in a single step
• Concatenate – Join together sequences and alignments with intelligent concatenation functions
• Batch rename – Change the text of any field in the metadata of Geneious Pro with the batch rename functionality.
• Alignment stripping – Strip gap-only and non-variable sites from alignments
• Basic manipulation – Extract, reverse-complement and translate whole sequences or selected sub-sequences
• Back translate – Back translate from protein to DNA (powered by EMBOSS)
• Reverse complement – Reverse complement (R.C.) any DNA or RNA sequence with a single click.
• in silico modification – Generate, mutate and shuffle sequences (powered by EMBOSS)
• Transfer annotations – Automatically transfer annotations to a reference sequence from BLAST hits or aligned sequences
• Stretch annotations – Select an annotation and move its left or right border to a new position by stretching it.
• Extract annotations – Extract all annotations of a single type to a sequence list document or a group of individual sequences.
• Ligate sequences – Ligate two sequences together, or re-circularize a single sequence by ligation.

Real-time Prediction Graphs and Analyses

When viewing sequences and alignments in Geneious Pro it is possible to turn on several analysis features which are performed in real-time, meaning they are updated immediately as you change settings and edit the data.

• Dynamic DNA translation – Translate and complement in real-time alongside your nucleotide sequences. Translate in any frame or up to 6 frames at once! Or just translate the annotation or selection that you're interested in.
• Generate 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
• Graphs on DNA sequences – Predict identity, read coverage, numerous statistics on base frequencies, residue frequencies, CpG islands and more
• Graphs on protein sequences – Predict molecular weight, isoelectric point, hydrophobicity, transmembrane regions, coiled coil regions, amino acid charge and more

Real-time Annotations

As well as being able to rapidly select and annotate custom regions, Geneious Pro has several functions for automatically determining regions of interest.

• Open reading frames – Turn on the ORF finder to predict open reading frames in real-time on any DNA sequence or alignment
• Heterozygous base calls – Install the heterozygotes plugin and make heterozygous base calls from your chromatogram data
• Restriction enzymes – Show the cutting positions on your sequence for all enzymes in your enzyme list
• Protein secondary structure - Dynamically predict the secondary structure of protein sequences using the EMBOSS tool Garnier

Predict Permanent Annotations

For more computationally intense operations, Geneious Pro can also predict and annotate features as a one-time event, then you can toggle whether or not they're displayed as annotations after that.

• SNP and variant finder – Predict all SNPS, INDELs and CNVs on an entire genome, a multiple alignment or an assembly
• ORF prediction with GLIMMER – Use GLIMMER to accurately predict ORFs on bacterial and viral genomes. Over 100 published genomes have already used GLIMMER.
• Tandem repeat finding with Phobos – Use the powerful Phobos plugin to find new tandem repeat regions in your genome
• EMBOSS predictions – Predict antigenic regions, protein secondary structure, transcription factors, signal cleavage sequences and more using EMBOOS tools
• High/low coverage finder – Identify regions of high and low coverage to perform your analyses with confidence