How do I create a pairwise DNA alignment?
The SnapGene pairwise alignment tool uses Parasail to align and compare two DNA and/or RNA sequences.
Parasail provides three alignment methods:
- Local Alignment
- Global Alignment
- Semi-Global alignment
In SnapGene click Tools → Align Sequences → Summary of Alignment Algorithms to learn about Parasail.
Note that the pairwise alignment tool does not check or automatically flip nucleotide sequences so that all are in the appropriate orientation. You should examine each sequence to confirm orientation, flip a sequence if required, then perform the alignment.
Option 1: Start from a Project
Open a folder containing the sequences for alignment as a project. See Use the SnapGene Project Interface.
Select two sequences in the side panel.
Click Annotate, simulate, or edit data → Align DNA Sequences.
Option 2: Start with Individual Files
Click Tools → Align Sequences → Align Two DNA Sequences....
If the two sequences for alignment are open as tabs in the SnapGene window then they will automatically be loaded as the input for pairwise alignment.
- If required set the two sequences for alignment. Use any combination of the following methods to add each sequence:
- Paste DNA sequences into the fields provided.
- Drag individual sequence files into the fields provided.
- Click the "Choose" dropdown and select a "Recent DNA file".
- Click the "Choose" dropdown and Browse to specify a sequence located somewhere on your computer.
- Click the Import button to import a sequence from NCBI (using an accession number).
- Set the algorithm or algorithms to use for pairwise alignment.
Enter a name for the new alignment file.
Click Align to create the alignment.
SnapGene provides three pairwise alignment algorithms. An alignment file can contain three separate alignments.
Click menu Tools → Align Sequences → Summary of Alignment Algorithms to learn more about each pairwise algorithm.
View the Alignment
If more than one alignment algorithm was selected then use the "Aligned using" dropdown to switch and view each alignment.
Click a disclosure triangle to view features associated with a sequence and see a number line.
Check the option to show the "Side Panel".
Configure how differences between the sequences are displayed using the "Format" drop-down in the side panel.
View key information about the alignment.
If required, add a description of the alignment in the side panel.
Save the Alignment
Click File → Save to save the alignment to an appropriate location on your computer.