Pairwise Alignment in Geneious Prime

This pairwise alignment series shows how to align two DNA sequences in Geneious Prime, tuning gap penalty and cost matrix settings and resolving inverted regions. A companion video covers reading dot plots to spot repeated regions, inversions, and translocations before aligning. The series spans two videos, 3 to 5 minutes each.

Course Content

Use Dot Plots to Explore Pairwise Relationships

Pairwise Alignment of DNA Sequences

Use Dot Plots to Explore Pairwise Relationships

Visualize sequence similarity beyond what alignment can show. Read dot plots in Geneious Prime, adjust word size and sensitivity, and identify repeated regions, inversions, and translocations between two sequences.

LENGTH 3 minutes

Pairwise Alignment of DNA Sequences

Align two DNA sequences using the Geneious alignment method, then tune the gap penalty and cost matrix to favor gaps over mismatches. Learn to detect and resolve inverted regions, which standard pairwise alignment cannot align directly.

LENGTH 5 minutes

Recommended Resources

What function should I use?

The difference between Pairwise/Multiple alignment, de novo Assembly, and Map to Reference.

Which multiple alignment algorithm should I use?

Four different multiple alignment algorithms are available in Geneious Prime.

Can I call SNPs on individual sequences aligned to a reference?

Learn how to call SNPs on the pairwise alignment/assembly.

Manual for Pairwise Alignment

A guide to using pairwise alignment in Geneious.

More Geneious Academy

TUTORIALHow to Compare Pairwise Alignment in Geneious Prime

Compare Salmonella and E. coli genomes with dot plots, then align a pygmy chimp sequence against a mutated copy.

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VIDEO SERIESMultiple Alignments in Geneious Prime

Choose the right alignment algorithm for your dataset size, from Muscle to MAFFT, then align multiple sequences and assess homology in Geneious Prime.

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