How do I create a pairwise protein alignment?
The SnapGene pairwise alignment tool uses Parasail to align and compare two protein sequences.
Parasail provides three alignment methods:
- Local Alignment
- Global Alignment
- Semi-Global alignment
Click Tools → Align Sequences → Summary of Alignment Algorithms to learn aboutParasail.
Option 1: Start from a Project
Open a folder containing the protein 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 Protein 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 protein sequences into the fields provided.
- Drag individual protein sequence files into the fields provided.
- Click the "Choose" dropdown and select a "Recent Protein file".
- Click the "Choose" dropdown and Browse to specify a protein sequence located somewhere on your computer.
- Click the Import button to import a sequence from NCBI or Uniprot (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.
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 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 the "Side Panel" to 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.