Pairwise Alignment

Use a dot plot to view regions of similarity then determine homology with pairwise alignment of related sequences.

Course Content

Pairwise Alignment Dot Plots

View and customize dot plots, view sequence inversions and repeating patterns in the sequence.
3 minutes

Pairwise Alignment of DNA Sequences

How to perform a pairwise alignment, choose an alignment algorithm and optimize and refine your alignments.
6 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

Use this practical exercise to align pairs of DNA and protein sequences using dot plots and alignment algorithms.
Watch how to perform multiple alignments and assess levels of homology among sequences before constructing a phylogeny.
Watch the series and learn how to use the Mauve plugin. Align genomes and convert alignments into standard alignments.
Watch the series on how to access GenBank, and prepare and submit sequences and alignments to the GenBank database.
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